remove trailing whitespace
This commit is contained in:
Axel Kohlmeyer
@ -41,9 +41,9 @@ should be -option=value (e.g. -border=5).
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-border add border to all sides of simulation box [default: 0 A]
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-border add border to all sides of simulation box [default: 0 A]
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-ax rotation around x-axis
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-ax rotation around x-axis
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-ay rotation around y-axis
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-ay rotation around y-axis
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-az rotation around z-axis
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-az rotation around z-axis
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-cd correction for dihedral for carbohydrate systems
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-cd correction for dihedral for carbohydrate systems
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-cmap add CMAP section to data file and fix cmap command lines in
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-cmap add CMAP section to data file and fix cmap command lines in
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input script" (NOTE: requires use of *.pdb file)
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input script" (NOTE: requires use of *.pdb file)
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In the "example" folder, you will find example files that were created
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In the "example" folder, you will find example files that were created
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@ -69,26 +69,26 @@ file has to the corresponding names in the charmm FF files. You'll
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need to add a "pdbalias residue x xnew" line for each change that
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need to add a "pdbalias residue x xnew" line for each change that
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needs to be made. The *.pgn should contain something like this:
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needs to be made. The *.pgn should contain something like this:
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package require psfgen
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package require psfgen
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topology top_all27_na.rtf
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topology top_all27_na.rtf
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pdbalias residue A ADE
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pdbalias residue A ADE
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pdbalias residue T THY
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pdbalias residue T THY
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pdbalias residue G GUA
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pdbalias residue G GUA
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pdbalias residue C CYT
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pdbalias residue C CYT
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.
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.
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.
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.
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.
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.
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segment A {pdb 1ac7_pared.pdb}
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segment A {pdb 1ac7_pared.pdb}
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coordpdb 1ac7_pared.pdb A
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coordpdb 1ac7_pared.pdb A
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guesscoord
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guesscoord
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writepdb 1ac7.pdb
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writepdb 1ac7.pdb
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writepsf charmm 1ac7.psf
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writepsf charmm 1ac7.psf
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exit
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exit
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5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
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5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
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1ac7.pdb file.
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1ac7.pdb file.
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6) Run charmm2lammps.pl by typing:
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6) Run charmm2lammps.pl by typing:
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"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"
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"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"
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7) Run lammps by typing: "lmp < 1ac7.in"
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7) Run lammps by typing: "lmp < 1ac7.in"
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@ -105,7 +105,7 @@ molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
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can be visualized in a standard visualization package such as VMD. The
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can be visualized in a standard visualization package such as VMD. The
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-charmm option put comments into the LAMMPS data file (everything
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-charmm option put comments into the LAMMPS data file (everything
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after the # sign is a comment) for user convenience in tracking atom
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after the # sign is a comment) for user convenience in tracking atom
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types etc. according to CHARMM nomenclature.
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types etc. according to CHARMM nomenclature.
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The example molecule provided above (i.e., 1ac7) is a DNA fragment.
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The example molecule provided above (i.e., 1ac7) is a DNA fragment.
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If instead, a peptide longer than 2 amino acid residues or a protein
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If instead, a peptide longer than 2 amino acid residues or a protein
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@ -10,7 +10,7 @@
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# 20050212 Needed (in the same directory):
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# 20050212 Needed (in the same directory):
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# - $project.crd ; Assumed to be correct and running
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# - $project.crd ; Assumed to be correct and running
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# - $project.psf ; CHARMM configs
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# - $project.psf ; CHARMM configs
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# - top_$forcefield.rtf ;
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# - top_$forcefield.rtf ;
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# - par_$forcefield.prm ;
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# - par_$forcefield.prm ;
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# Ouput:
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# Ouput:
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# - $project.data ; LAMMPS data file
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# - $project.data ; LAMMPS data file
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@ -41,10 +41,10 @@
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#
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#
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# General Many thanks to Paul S. Crozier for checking script validity
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# General Many thanks to Paul S. Crozier for checking script validity
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# against his projects.
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# against his projects.
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# Also thanks to Xiaohu Hu (hux2@ornl.gov) and Robert A. Latour
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# Also thanks to Xiaohu Hu (hux2@ornl.gov) and Robert A. Latour
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# (latourr@clemson.edu), David Hyde-Volpe, and Tigran Abramyan,
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# (latourr@clemson.edu), David Hyde-Volpe, and Tigran Abramyan,
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# Clemson University and Chris Lorenz (chris.lorenz@kcl.ac.uk),
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# Clemson University and Chris Lorenz (chris.lorenz@kcl.ac.uk),
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# King's College London for their efforts to add CMAP sections,
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# King's College London for their efforts to add CMAP sections,
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# which is implemented using the option flag "-cmap".
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# which is implemented using the option flag "-cmap".
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# Initialization
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# Initialization
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@ -52,7 +52,7 @@
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sub Test
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sub Test
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{
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{
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my $name = shift(@_);
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my $name = shift(@_);
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printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
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printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
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return !scalar(stat($name));
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return !scalar(stat($name));
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}
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}
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@ -63,7 +63,7 @@
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my $k = 0;
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my $k = 0;
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my @dir = ("x", "y", "z");
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my @dir = ("x", "y", "z");
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my @options = ("-help", "-nohints", "-water", "-ions", "-center",
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my @options = ("-help", "-nohints", "-water", "-ions", "-center",
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"-quiet", "-pdb_ctrl", "-l", "-lx", "-ly", "-lz",
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"-quiet", "-pdb_ctrl", "-l", "-lx", "-ly", "-lz",
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"-border", "-ax", "-ay", "-az", "-cmap");
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"-border", "-ax", "-ay", "-az", "-cmap");
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my @remarks = ("display this message",
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my @remarks = ("display this message",
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"do not print type and style hints in data file",
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"do not print type and style hints in data file",
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@ -83,7 +83,7 @@
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"generate a CMAP section in data file"
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"generate a CMAP section in data file"
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);
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);
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my $notes;
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my $notes;
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$program = "charmm2lammps";
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$program = "charmm2lammps";
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$version = "1.9.0";
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$version = "1.9.0";
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$year = "2016";
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$year = "2016";
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@ -99,7 +99,7 @@
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$L = (0, 0, 0);
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$L = (0, 0, 0);
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$cmap = 0;
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$cmap = 0;
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@R = M_Unit();
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@R = M_Unit();
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$notes = " * The average of extremes is used as the origin\n";
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$notes = " * The average of extremes is used as the origin\n";
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$notes .= " * Residues are numbered sequentially\n";
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$notes .= " * Residues are numbered sequentially\n";
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$notes .= " * Water is added on an FCC lattice: allow 5 ps for";
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$notes .= " * Water is added on an FCC lattice: allow 5 ps for";
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@ -119,7 +119,7 @@
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$notes .= " - project.data LAMMPS data file\n";
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$notes .= " - project.data LAMMPS data file\n";
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$notes .= " - project.in suggested LAMMPS input script\n";
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$notes .= " - project.in suggested LAMMPS input script\n";
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$notes .= " - project_ctrl.pdb control file when requested\n";
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$notes .= " - project_ctrl.pdb control file when requested\n";
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foreach (@ARGV)
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foreach (@ARGV)
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{
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{
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if (substr($_, 0, 1) eq "-")
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if (substr($_, 0, 1) eq "-")
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@ -200,7 +200,7 @@
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return "{".$v[0].", ".$v[1].", ".$v[2]."}";
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return "{".$v[0].", ".$v[1].", ".$v[2]."}";
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}
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}
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sub V_Add
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sub V_Add
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{
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{
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my @v1 = splice(@_, 0, 3);
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my @v1 = splice(@_, 0, 3);
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@ -208,8 +208,8 @@
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return ($v1[0]+$v2[0], $v1[1]+$v2[1], $v1[2]+$v2[2]);
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return ($v1[0]+$v2[0], $v1[1]+$v2[1], $v1[2]+$v2[2]);
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}
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}
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sub V_Subtr
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sub V_Subtr
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{
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{
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my @v1 = splice(@_, 0, 3);
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my @v1 = splice(@_, 0, 3);
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@ -217,8 +217,8 @@
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return ($v1[0]-$v2[0], $v1[1]-$v2[1], $v1[2]-$v2[2]);
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return ($v1[0]-$v2[0], $v1[1]-$v2[1], $v1[2]-$v2[2]);
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}
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}
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sub V_Dot
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sub V_Dot
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{
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{
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my @v1 = splice(@_, 0, 3);
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my @v1 = splice(@_, 0, 3);
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@ -226,8 +226,8 @@
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return $v1[0]*$v2[0]+$v1[1]*$v2[1]+$v1[2]*$v2[2];
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return $v1[0]*$v2[0]+$v1[1]*$v2[1]+$v1[2]*$v2[2];
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}
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}
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sub V_Mult
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sub V_Mult
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{
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{
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my @v = splice(@_, 0, 3);
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my @v = splice(@_, 0, 3);
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@ -236,12 +236,12 @@
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return ($f*$v[0], $f*$v[1], $f*$v[2]);
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return ($f*$v[0], $f*$v[1], $f*$v[2]);
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}
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}
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sub M_String
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sub M_String
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{
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{
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my $string;
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my $string;
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for (my $i=0; $i<3; ++$i)
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for (my $i=0; $i<3; ++$i)
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{
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{
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$string .= ", " if ($i);
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$string .= ", " if ($i);
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$string .= V_String(splice(@_, 0, 3));
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$string .= V_String(splice(@_, 0, 3));
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@ -258,7 +258,7 @@
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@_[2], @_[5], @_[8]);
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@_[2], @_[5], @_[8]);
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}
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}
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sub M_Dot
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sub M_Dot
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{
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{
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my @v11 = splice(@_, 0, 3);
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my @v11 = splice(@_, 0, 3);
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@ -268,7 +268,7 @@
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my @v21 = splice(@m, 0, 3);
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my @v21 = splice(@m, 0, 3);
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my @v22 = splice(@m, 0, 3);
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my @v22 = splice(@m, 0, 3);
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my @v23 = splice(@m, 0, 3);
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my @v23 = splice(@m, 0, 3);
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return (
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return (
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V_Dot(@v11, @v21), V_Dot(@v11, @v22), V_Dot(@v11, @v23),
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V_Dot(@v11, @v21), V_Dot(@v11, @v22), V_Dot(@v11, @v23),
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V_Dot(@v12, @v21), V_Dot(@v12, @v22), V_Dot(@v12, @v23),
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V_Dot(@v12, @v21), V_Dot(@v12, @v22), V_Dot(@v12, @v23),
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@ -279,7 +279,7 @@
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sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
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sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
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sub PI { return 4*atan2(1,1); }
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sub PI { return 4*atan2(1,1); }
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sub M_Rotate
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sub M_Rotate
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{ # vmd convention
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{ # vmd convention
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my $n = shift(@_);
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my $n = shift(@_);
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@ -294,7 +294,7 @@
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return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
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return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
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return M_Unit();
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return M_Unit();
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}
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}
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sub MV_Dot
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sub MV_Dot
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{
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{
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@ -305,10 +305,10 @@
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return (V_Dot(@v11, @v2), V_Dot(@v12, @v2), V_Dot(@v13, @v2));
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return (V_Dot(@v11, @v2), V_Dot(@v12, @v2), V_Dot(@v13, @v2));
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}
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}
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# CHARMM input
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# CHARMM input
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sub PSFConnectivity
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sub PSFConnectivity
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{
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{
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my $n = PSFGoto(bonds);
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my $n = PSFGoto(bonds);
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@ -353,8 +353,8 @@
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$dihedral_flag = 1;
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$dihedral_flag = 1;
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return $ndihedral;
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return $ndihedral;
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}
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}
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sub CreatePSFIndex # make an index of id
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sub CreatePSFIndex # make an index of id
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{ # locations
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{ # locations
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my @psf_ids = ("!NATOM","!NBOND:","!NTHETA:","!NPHI:","!NIMPHI:");
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my @psf_ids = ("!NATOM","!NBOND:","!NTHETA:","!NPHI:","!NIMPHI:");
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@ -374,13 +374,13 @@
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}
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}
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}
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}
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sub PSFGoto # goto $ident in <PSF>
|
sub PSFGoto # goto $ident in <PSF>
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{
|
{
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CreatePSFIndex() if (!scalar(%PSFIndex));
|
CreatePSFIndex() if (!scalar(%PSFIndex));
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my $id = shift(@_);
|
my $id = shift(@_);
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my @n = split(" ", $PSFIndex{$id});
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my @n = split(" ", $PSFIndex{$id});
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|
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@PSFBuffer = ();
|
@PSFBuffer = ();
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# return PSFDihedrals() if ($id eq "dihedrals");
|
# return PSFDihedrals() if ($id eq "dihedrals");
|
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if (!scalar(@n))
|
if (!scalar(@n))
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||||||
@ -415,10 +415,10 @@
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|||||||
{
|
{
|
||||||
my $items = shift(@_);
|
my $items = shift(@_);
|
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my $n = $items;
|
my $n = $items;
|
||||||
|
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if ($psf_ncols>7) { printf(PSF_CTRL "\n"); $psf_ncols = 0; }
|
if ($psf_ncols>7) { printf(PSF_CTRL "\n"); $psf_ncols = 0; }
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foreach(@_)
|
foreach(@_)
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{
|
{
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printf(PSF_CTRL " %7d", $_);
|
printf(PSF_CTRL " %7d", $_);
|
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++$psf_ncols;
|
++$psf_ncols;
|
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if ((!--$n) && ($psf_ncols>7))
|
if ((!--$n) && ($psf_ncols>7))
|
||||||
@ -434,7 +434,7 @@
|
|||||||
sub CRDGoto
|
sub CRDGoto
|
||||||
{
|
{
|
||||||
my $n;
|
my $n;
|
||||||
|
|
||||||
return if (shift(@_) ne "atoms");
|
return if (shift(@_) ne "atoms");
|
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open(CRD, "<".($pdb ? $Pdb : $Crd)) if (fileno(CRD) eq "");
|
open(CRD, "<".($pdb ? $Pdb : $Crd)) if (fileno(CRD) eq "");
|
||||||
seek(CRD, 0, SEEK_SET);
|
seek(CRD, 0, SEEK_SET);
|
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@ -451,20 +451,20 @@
|
|||||||
my @data = ();
|
my @data = ();
|
||||||
my $c = 0;
|
my $c = 0;
|
||||||
my $line;
|
my $line;
|
||||||
|
|
||||||
while (substr($line = <CRD>, 0, 4) ne "ATOM") {};
|
while (substr($line = <CRD>, 0, 4) ne "ATOM") {};
|
||||||
chop($line);
|
chop($line);
|
||||||
foreach (@n) { push(@data, substr($line, ($c += $_)-$_, $_)); }
|
foreach (@n) { push(@data, substr($line, ($c += $_)-$_, $_)); }
|
||||||
return @data[1, 8, 5, 3, 11, 12, 13, 17, 8, 15];
|
return @data[1, 8, 5, 3, 11, 12, 13, 17, 8, 15];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub Delete
|
sub Delete
|
||||||
{
|
{
|
||||||
my $item = shift(@_);
|
my $item = shift(@_);
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
my @list;
|
my @list;
|
||||||
|
|
||||||
foreach (@_)
|
foreach (@_)
|
||||||
{
|
{
|
||||||
my @tmp = split(" ");
|
my @tmp = split(" ");
|
||||||
@ -483,9 +483,9 @@
|
|||||||
my $flag = $list[0] gt $list[-1];
|
my $flag = $list[0] gt $list[-1];
|
||||||
my $j = $n;
|
my $j = $n;
|
||||||
my $tmp;
|
my $tmp;
|
||||||
|
|
||||||
return "" if (scalar(@list)<$n);
|
return "" if (scalar(@list)<$n);
|
||||||
$flag = $list[1] gt $list[-2]
|
$flag = $list[1] gt $list[-2]
|
||||||
if ((scalar(@list)>3)&&($list[0] eq $list[-1]));
|
if ((scalar(@list)>3)&&($list[0] eq $list[-1]));
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
@ -506,7 +506,7 @@
|
|||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
my @tmp = split(" ", <PSF>);
|
my @tmp = split(" ", <PSF>);
|
||||||
$tmp[5] = $symbols{$tmp[5]}
|
$tmp[5] = $symbols{$tmp[5]}
|
||||||
if ((substr($tmp[5],0,1) lt '0')||(substr($tmp[5],0,1) gt '9'));
|
if ((substr($tmp[5],0,1) lt '0')||(substr($tmp[5],0,1) gt '9'));
|
||||||
push(@atom_types, $tmp[5]);
|
push(@atom_types, $tmp[5]);
|
||||||
++$list{$tmp[5]};
|
++$list{$tmp[5]};
|
||||||
@ -524,7 +524,7 @@
|
|||||||
return sort({$a<=>$b} keys(%list));
|
return sort({$a<=>$b} keys(%list));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub Markers
|
sub Markers
|
||||||
{
|
{
|
||||||
my %markers = (
|
my %markers = (
|
||||||
@ -543,14 +543,14 @@
|
|||||||
{
|
{
|
||||||
my @cols = @_;
|
my @cols = @_;
|
||||||
my $f = (scalar(@cols)>3)&&(substr($cols[3],0,1) ne "!");
|
my $f = (scalar(@cols)>3)&&(substr($cols[3],0,1) ne "!");
|
||||||
my @tmp = (-$cols[1], $cols[2],
|
my @tmp = (-$cols[1], $cols[2],
|
||||||
$f ? -$cols[4]:-$cols[1], $f ? $cols[5]:$cols[2]);
|
$f ? -$cols[4]:-$cols[1], $f ? $cols[5]:$cols[2]);
|
||||||
$tmp[1] *= 2.0**(5/6); # adjust sigma
|
$tmp[1] *= 2.0**(5/6); # adjust sigma
|
||||||
$tmp[3] *= 2.0**(5/6); # adjust sigma 1-4
|
$tmp[3] *= 2.0**(5/6); # adjust sigma 1-4
|
||||||
return join(" ", @tmp);
|
return join(" ", @tmp);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub AtomParameters # non-bonded parameters
|
sub AtomParameters # non-bonded parameters
|
||||||
{
|
{
|
||||||
my @types;
|
my @types;
|
||||||
@ -574,7 +574,7 @@
|
|||||||
if ($markers{$cols[0]} ne "") {
|
if ($markers{$cols[0]} ne "") {
|
||||||
$read = ($markers{$cols[0]} eq "0") ? 1 : 0; }
|
$read = ($markers{$cols[0]} eq "0") ? 1 : 0; }
|
||||||
}
|
}
|
||||||
$list[$types{HT}] = NonBond(0, -0.046, 0.2245)
|
$list[$types{HT}] = NonBond(0, -0.046, 0.2245)
|
||||||
if ($water_dens&&($list[$types{HT}] eq ""));
|
if ($water_dens&&($list[$types{HT}] eq ""));
|
||||||
$list[$types{OT}] = NonBond(0, -0.152100, 1.768200)
|
$list[$types{OT}] = NonBond(0, -0.152100, 1.768200)
|
||||||
if ($water_dens&&($list[$types{OT}] eq ""));
|
if ($water_dens&&($list[$types{OT}] eq ""));
|
||||||
@ -593,7 +593,7 @@
|
|||||||
my $id = (bonds, angles, dihedrals, impropers)[$mode];
|
my $id = (bonds, angles, dihedrals, impropers)[$mode];
|
||||||
my $n = PSFGoto($id);
|
my $n = PSFGoto($id);
|
||||||
my %list;
|
my %list;
|
||||||
|
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
my @tmp = ();
|
my @tmp = ();
|
||||||
@ -624,7 +624,7 @@
|
|||||||
{ # <PARAMETERS>
|
{ # <PARAMETERS>
|
||||||
my $mode = shift(@_); # bonded mode
|
my $mode = shift(@_); # bonded mode
|
||||||
return if (($mode>3)||($mode<0));
|
return if (($mode>3)||($mode<0));
|
||||||
|
|
||||||
my $items = (2, 3, 4, 4)[$mode]; # items per entry
|
my $items = (2, 3, 4, 4)[$mode]; # items per entry
|
||||||
my $name = ("bond", "angle", "dihedral", "improper")[$mode];
|
my $name = ("bond", "angle", "dihedral", "improper")[$mode];
|
||||||
my $read = 0;
|
my $read = 0;
|
||||||
@ -691,7 +691,7 @@
|
|||||||
}
|
}
|
||||||
for (my $i=0; $i<scalar(@types); ++$i)
|
for (my $i=0; $i<scalar(@types); ++$i)
|
||||||
{
|
{
|
||||||
printf("Warning: %s parameter %4d for [%s] was not found\n",
|
printf("Warning: %s parameter %4d for [%s] was not found\n",
|
||||||
$name, $i+1, $types[$i]) if ($parms[$i] eq "");
|
$name, $i+1, $types[$i]) if ($parms[$i] eq "");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -702,7 +702,7 @@
|
|||||||
my $id = shift(@_);
|
my $id = shift(@_);
|
||||||
my $value = shift(@_);
|
my $value = shift(@_);
|
||||||
my $new = "";
|
my $new = "";
|
||||||
|
|
||||||
foreach (split(":", $parms[$id]))
|
foreach (split(":", $parms[$id]))
|
||||||
{
|
{
|
||||||
my @tmp = split(" ");
|
my @tmp = split(" ");
|
||||||
@ -712,8 +712,8 @@
|
|||||||
}
|
}
|
||||||
$parms[$id] = $new;
|
$parms[$id] = $new;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub CorrectDihedralParameters
|
sub CorrectDihedralParameters
|
||||||
{
|
{
|
||||||
my $n = PSFGoto(dihedrals);
|
my $n = PSFGoto(dihedrals);
|
||||||
@ -723,7 +723,7 @@
|
|||||||
my $id2;
|
my $id2;
|
||||||
my $first;
|
my $first;
|
||||||
my $last;
|
my $last;
|
||||||
|
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
my @bonded = PSFGet(4);
|
my @bonded = PSFGet(4);
|
||||||
@ -733,7 +733,7 @@
|
|||||||
$first = $bonded[0];
|
$first = $bonded[0];
|
||||||
$last = $bonded[3];
|
$last = $bonded[3];
|
||||||
if ($first>$last) { my $tmp = $first; $first = $last; $last = $tmp; }
|
if ($first>$last) { my $tmp = $first; $first = $last; $last = $tmp; }
|
||||||
if (($id2 = $hash{$hash_id = $first." ".$last}) eq "")
|
if (($id2 = $hash{$hash_id = $first." ".$last}) eq "")
|
||||||
{
|
{
|
||||||
$hash{$hash_id} = $id1; # add id to hash
|
$hash{$hash_id} = $id1; # add id to hash
|
||||||
}
|
}
|
||||||
@ -757,26 +757,26 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub AddMass
|
sub AddMass
|
||||||
{
|
{
|
||||||
my $symbol = shift(@_);
|
my $symbol = shift(@_);
|
||||||
my $mass = shift(@_);
|
my $mass = shift(@_);
|
||||||
|
|
||||||
return if ($symbols{$symbol} ne "");
|
return if ($symbols{$symbol} ne "");
|
||||||
$ids{++$max_id} = $symbol;
|
$ids{++$max_id} = $symbol;
|
||||||
$masses{$max_id} = $mass;
|
$masses{$max_id} = $mass;
|
||||||
$symbols{$symbol} = $max_id;
|
$symbols{$symbol} = $max_id;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub ReadTopology # read topology links
|
sub ReadTopology # read topology links
|
||||||
{
|
{
|
||||||
my $id = shift(@_);
|
my $id = shift(@_);
|
||||||
my $item = shift(@_);
|
my $item = shift(@_);
|
||||||
my $read = 0;
|
my $read = 0;
|
||||||
my @tmp;
|
my @tmp;
|
||||||
|
|
||||||
open(TOPOLOGY, "<top_$forcefield.rtf");
|
open(TOPOLOGY, "<top_$forcefield.rtf");
|
||||||
$max_id = 0;
|
$max_id = 0;
|
||||||
while (<TOPOLOGY>)
|
while (<TOPOLOGY>)
|
||||||
@ -821,7 +821,7 @@
|
|||||||
my @z = (-$L[2]/2, $L[2]/2);
|
my @z = (-$L[2]/2, $L[2]/2);
|
||||||
my $n = CRDGoto(atoms);
|
my $n = CRDGoto(atoms);
|
||||||
my $extremes = !($L[0] && $L[1] && $L[2]);
|
my $extremes = !($L[0] && $L[1] && $L[2]);
|
||||||
|
|
||||||
@Center = (0, 0, 0);
|
@Center = (0, 0, 0);
|
||||||
return if (!$n);
|
return if (!$n);
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
@ -858,7 +858,7 @@
|
|||||||
my $s_OT = 1.7682; # CHARMM sigma [A]
|
my $s_OT = 1.7682; # CHARMM sigma [A]
|
||||||
my $ahoh = (180-104.52)/360*PI();
|
my $ahoh = (180-104.52)/360*PI();
|
||||||
my @p = ($loh*cos($ahoh), $loh*sin($ahoh), 0);
|
my @p = ($loh*cos($ahoh), $loh*sin($ahoh), 0);
|
||||||
|
|
||||||
printf("Info: creating fcc water\n") if ($info);
|
printf("Info: creating fcc water\n") if ($info);
|
||||||
$n_water = 4; # molecules/cell
|
$n_water = 4; # molecules/cell
|
||||||
$nav = 6.022e23; # 1/mol
|
$nav = 6.022e23; # 1/mol
|
||||||
@ -867,11 +867,11 @@
|
|||||||
@p_water = (0,0,0, @p, -$p[0],$p[1],0);
|
@p_water = (0,0,0, @p, -$p[0],$p[1],0);
|
||||||
$v_fcc = $n_water*$v_water; # cell volume
|
$v_fcc = $n_water*$v_water; # cell volume
|
||||||
$l_fcc = $v_fcc**(1/3); # cell length
|
$l_fcc = $v_fcc**(1/3); # cell length
|
||||||
@p_fcc = (0.00,0.00,0.00, 0.50,0.50,0.00,
|
@p_fcc = (0.00,0.00,0.00, 0.50,0.50,0.00,
|
||||||
0.50,0.00,0.50, 0.00,0.50,0.50);
|
0.50,0.00,0.50, 0.00,0.50,0.50);
|
||||||
@n_fcc = ();
|
@n_fcc = ();
|
||||||
for (my $i=0; $i<scalar(@L); ++$i)
|
for (my $i=0; $i<scalar(@L); ++$i)
|
||||||
{
|
{
|
||||||
my $n = $L[$i]/$l_fcc; # calculate n_fcc
|
my $n = $L[$i]/$l_fcc; # calculate n_fcc
|
||||||
$n = int($n-int($n) ? $n+1 : $n); # ceil($n)
|
$n = int($n-int($n) ? $n+1 : $n); # ceil($n)
|
||||||
$L[$i] = $n*$l_fcc; # adjust box length
|
$L[$i] = $n*$l_fcc; # adjust box length
|
||||||
@ -894,18 +894,18 @@
|
|||||||
return $x>0 ? int($x) : int($x)-1;
|
return $x>0 ? int($x) : int($x)-1;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub Periodic
|
sub Periodic
|
||||||
{
|
{
|
||||||
my @p = splice(@_, 0, 3);
|
my @p = splice(@_, 0, 3);
|
||||||
|
|
||||||
return (
|
return (
|
||||||
$p[0]-floor($p[0]/$L[0]+0.5)*$L[0],
|
$p[0]-floor($p[0]/$L[0]+0.5)*$L[0],
|
||||||
$p[1]-floor($p[1]/$L[1]+0.5)*$L[1],
|
$p[1]-floor($p[1]/$L[1]+0.5)*$L[1],
|
||||||
$p[2]-floor($p[2]/$L[2]+0.5)*$L[2]);
|
$p[2]-floor($p[2]/$L[2]+0.5)*$L[2]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub EraseWater
|
sub EraseWater
|
||||||
{
|
{
|
||||||
my $r = shift(@_)/2;
|
my $r = shift(@_)/2;
|
||||||
@ -918,7 +918,7 @@
|
|||||||
$p[0]+$r,$p[1]+$r,$p[2]-$r, $p[0]+$r,$p[1]+$r,$p[2]+$r);
|
$p[0]+$r,$p[1]+$r,$p[2]-$r, $p[0]+$r,$p[1]+$r,$p[2]+$r);
|
||||||
my %list;
|
my %list;
|
||||||
my @n;
|
my @n;
|
||||||
|
|
||||||
my $d2 = ($r_water+$r)**2;
|
my $d2 = ($r_water+$r)**2;
|
||||||
my @l = ($L[0]/2, $L[1]/2, $L[2]/2);
|
my @l = ($L[0]/2, $L[1]/2, $L[2]/2);
|
||||||
for (my $i=0; $i<scalar(@edges); $i+=3) # determine candidates
|
for (my $i=0; $i<scalar(@edges); $i+=3) # determine candidates
|
||||||
@ -946,8 +946,8 @@
|
|||||||
$flags_fcc[$n[0]][$n[1]][$n[2]] &= $flags; # set flags
|
$flags_fcc[$n[0]][$n[1]][$n[2]] &= $flags; # set flags
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub CountFCC
|
sub CountFCC
|
||||||
{
|
{
|
||||||
my $n = 0;
|
my $n = 0;
|
||||||
@ -964,11 +964,11 @@
|
|||||||
return ($n_fccs = $n);
|
return ($n_fccs = $n);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub AddIons
|
sub AddIons
|
||||||
{
|
{
|
||||||
my $n = ($n_waters = CountFCC())-int(abs($net_charge));
|
my $n = ($n_waters = CountFCC())-int(abs($net_charge));
|
||||||
|
|
||||||
return if (!$ions);
|
return if (!$ions);
|
||||||
printf("Warning: charge not neutralized: too little water\n") if ($n<0);
|
printf("Warning: charge not neutralized: too little water\n") if ($n<0);
|
||||||
return if ($n<0);
|
return if ($n<0);
|
||||||
@ -1008,7 +1008,7 @@
|
|||||||
$flags |= $salt*(1+$salt*$na)*$bit; # set type of ion
|
$flags |= $salt*(1+$salt*$na)*$bit; # set type of ion
|
||||||
}
|
}
|
||||||
};
|
};
|
||||||
$bit *= 2;
|
$bit *= 2;
|
||||||
}
|
}
|
||||||
$flags_fcc[$x][$y][$z] = $flags;
|
$flags_fcc[$x][$y][$z] = $flags;
|
||||||
}
|
}
|
||||||
@ -1016,7 +1016,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
# LAMMPS output
|
# LAMMPS output
|
||||||
|
|
||||||
sub WriteLAMMPSHeader # print lammps header
|
sub WriteLAMMPSHeader # print lammps header
|
||||||
@ -1053,12 +1053,12 @@
|
|||||||
printf(PSF_CTRL "\n");
|
printf(PSF_CTRL "\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub WriteBoxSize # print box limits
|
sub WriteBoxSize # print box limits
|
||||||
{
|
{
|
||||||
my @lo = V_Mult(@L[0,1,2], -1/2);
|
my @lo = V_Mult(@L[0,1,2], -1/2);
|
||||||
my @hi = V_Mult(@L[0,1,2], 1/2);
|
my @hi = V_Mult(@L[0,1,2], 1/2);
|
||||||
|
|
||||||
@lo = V_Add(@lo, @Center) if (!$center);
|
@lo = V_Add(@lo, @Center) if (!$center);
|
||||||
@hi = V_Add(@hi, @Center) if (!$center);
|
@hi = V_Add(@hi, @Center) if (!$center);
|
||||||
printf(LAMMPS "%12.8g %12.8g xlo xhi\n", $lo[0], $hi[0]);
|
printf(LAMMPS "%12.8g %12.8g xlo xhi\n", $lo[0], $hi[0]);
|
||||||
@ -1066,11 +1066,11 @@
|
|||||||
printf(LAMMPS "%12.8g %12.8g zlo zhi\n\n", $lo[2], $hi[2]);
|
printf(LAMMPS "%12.8g %12.8g zlo zhi\n\n", $lo[2], $hi[2]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub WriteMasses # print mass list
|
sub WriteMasses # print mass list
|
||||||
{
|
{
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
|
|
||||||
printf(LAMMPS "Masses\n\n");
|
printf(LAMMPS "Masses\n\n");
|
||||||
foreach (@types)
|
foreach (@types)
|
||||||
{
|
{
|
||||||
@ -1132,7 +1132,7 @@
|
|||||||
printf(PDB_CTRL "ATOM %6.6s %-4.4s %-3.3s %5.5s %3.3s ".
|
printf(PDB_CTRL "ATOM %6.6s %-4.4s %-3.3s %5.5s %3.3s ".
|
||||||
"%7.7s %7.7s %7.7s %5.5s %5.5s %4.4s %s\n", $k,
|
"%7.7s %7.7s %7.7s %5.5s %5.5s %4.4s %s\n", $k,
|
||||||
$types[$par[$j]-1], $n-1 ? "HOH" : "ION", $res, "",
|
$types[$par[$j]-1], $n-1 ? "HOH" : "ION", $res, "",
|
||||||
$xyz[0], $xyz[1], $xyz[2], "1.00", "0.00", "",
|
$xyz[0], $xyz[1], $xyz[2], "1.00", "0.00", "",
|
||||||
$n-1 ? "WATR" : "SALT") if ($pdb_ctrl);
|
$n-1 ? "WATR" : "SALT") if ($pdb_ctrl);
|
||||||
printf(PSF_CTRL "%8d %4.4s %-4.4s %-4.4s %-4.4s %4.4s ".
|
printf(PSF_CTRL "%8d %4.4s %-4.4s %-4.4s %-4.4s %4.4s ".
|
||||||
"%16.8e %7.7s %9.9s 0\n", $k, $n-1 ? "WATR" : "SALT",
|
"%16.8e %7.7s %9.9s 0\n", $k, $n-1 ? "WATR" : "SALT",
|
||||||
@ -1154,11 +1154,11 @@
|
|||||||
{
|
{
|
||||||
my $n = PSFGoto(atoms);
|
my $n = PSFGoto(atoms);
|
||||||
my @res = (0, 0);
|
my @res = (0, 0);
|
||||||
|
|
||||||
printf(PSF_CTRL "%8d !NATOM\n", $n+2*$n_waters+$n_fccs);
|
printf(PSF_CTRL "%8d !NATOM\n", $n+2*$n_waters+$n_fccs);
|
||||||
while (<PSF>)
|
while (<PSF>)
|
||||||
{
|
{
|
||||||
last if (!$n--);
|
last if (!$n--);
|
||||||
my @psf = split(" ");
|
my @psf = split(" ");
|
||||||
if ($res[1]!=$psf[2]) { ++$res[0]; $res[1] = $psf[2]; }
|
if ($res[1]!=$psf[2]) { ++$res[0]; $res[1] = $psf[2]; }
|
||||||
printf(PSF_CTRL "%8d %4.4s %-4.4s %-4.4s %-4.4s %-4.4s ".
|
printf(PSF_CTRL "%8d %4.4s %-4.4s %-4.4s %-4.4s %-4.4s ".
|
||||||
@ -1173,7 +1173,7 @@
|
|||||||
my $n = PSFGoto(atoms);
|
my $n = PSFGoto(atoms);
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
my @res = (0, 0);
|
my @res = (0, 0);
|
||||||
|
|
||||||
CRDGoto(atoms);
|
CRDGoto(atoms);
|
||||||
$net_charge = 0;
|
$net_charge = 0;
|
||||||
printf(LAMMPS "Atoms%s\n\n",($add ? " # full" : "")) if ($n>0);
|
printf(LAMMPS "Atoms%s\n\n",($add ? " # full" : "")) if ($n>0);
|
||||||
@ -1233,7 +1233,7 @@
|
|||||||
{
|
{
|
||||||
my @tmp = split(" ");
|
my @tmp = split(" ");
|
||||||
printf(LAMMPS "%8d", ++$k);
|
printf(LAMMPS "%8d", ++$k);
|
||||||
for (my $j=0; $j<$n; ++$j) {
|
for (my $j=0; $j<$n; ++$j) {
|
||||||
printf(LAMMPS " %16.12g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
|
printf(LAMMPS " %16.12g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
|
||||||
printf(LAMMPS "%s\n", $add ? " # ".$types[$i] : "");
|
printf(LAMMPS "%s\n", $add ? " # ".$types[$i] : "");
|
||||||
}
|
}
|
||||||
@ -1249,7 +1249,7 @@
|
|||||||
my $mode = shift(@_);
|
my $mode = shift(@_);
|
||||||
my $k = shift(@_);
|
my $k = shift(@_);
|
||||||
my $atom = $k_fcc;
|
my $atom = $k_fcc;
|
||||||
|
|
||||||
return $k if (($mode>1)||!$water_dens);
|
return $k if (($mode>1)||!$water_dens);
|
||||||
my $type = $mode ? CreateID(HT, OT, HT) : CreateID(HT, OT);
|
my $type = $mode ? CreateID(HT, OT, HT) : CreateID(HT, OT);
|
||||||
my $id = $link{$type};
|
my $id = $link{$type};
|
||||||
@ -1266,7 +1266,7 @@
|
|||||||
my $bit = 1;
|
my $bit = 1;
|
||||||
for (my $i=0; $i<scalar(@p_fcc); $i+=3)
|
for (my $i=0; $i<scalar(@p_fcc); $i+=3)
|
||||||
{
|
{
|
||||||
if ($flags&$bit)
|
if ($flags&$bit)
|
||||||
{
|
{
|
||||||
if ($flags&($bit*$salt)) { ++$atom; }
|
if ($flags&($bit*$salt)) { ++$atom; }
|
||||||
else
|
else
|
||||||
@ -1293,7 +1293,7 @@
|
|||||||
return $k;
|
return $k;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub WriteBonded # print bonded list
|
sub WriteBonded # print bonded list
|
||||||
{
|
{
|
||||||
my $mode = shift(@_);
|
my $mode = shift(@_);
|
||||||
@ -1304,7 +1304,7 @@
|
|||||||
my $k = 0;
|
my $k = 0;
|
||||||
my @delta;
|
my @delta;
|
||||||
my @tmp;
|
my @tmp;
|
||||||
|
|
||||||
return 0 if ($n<1);
|
return 0 if ($n<1);
|
||||||
printf(LAMMPS "%s\n\n", ucfirst($title));
|
printf(LAMMPS "%s\n\n", ucfirst($title));
|
||||||
printf(PSF_CTRL "\n%8d %s %s\n", $n+($mode ? ($mode==1 ? $n_waters : 0)
|
printf(PSF_CTRL "\n%8d %s %s\n", $n+($mode ? ($mode==1 ? $n_waters : 0)
|
||||||
@ -1349,7 +1349,7 @@
|
|||||||
return $k;
|
return $k;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub CreateCorrectedPairCoefficients
|
sub CreateCorrectedPairCoefficients
|
||||||
{
|
{
|
||||||
my $read = 0;
|
my $read = 0;
|
||||||
@ -1372,8 +1372,8 @@
|
|||||||
if (($id1 ne "")&&($id2 ne ""))
|
if (($id1 ne "")&&($id2 ne ""))
|
||||||
{
|
{
|
||||||
my @c = (abs($cols[2]), $cols[3]*2.0**(-1/6));
|
my @c = (abs($cols[2]), $cols[3]*2.0**(-1/6));
|
||||||
if ($type{$id2}<$type{$id1})
|
if ($type{$id2}<$type{$id1})
|
||||||
{
|
{
|
||||||
my $tmp = $id1; $id1 = $id2; $id2 = $tmp;
|
my $tmp = $id1; $id1 = $id2; $id2 = $tmp;
|
||||||
}
|
}
|
||||||
$coefficients .= ":" if ($coefficients ne "");
|
$coefficients .= ":" if ($coefficients ne "");
|
||||||
@ -1386,7 +1386,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub WriteData
|
sub WriteData
|
||||||
{
|
{
|
||||||
open(LAMMPS, ">$project.in"); # use .in for temporary
|
open(LAMMPS, ">$project.in"); # use .in for temporary
|
||||||
@ -1448,7 +1448,7 @@
|
|||||||
printf(LAMMPS "pair_style lj/charmm/coul/long 8 12\n");
|
printf(LAMMPS "pair_style lj/charmm/coul/long 8 12\n");
|
||||||
printf(LAMMPS "pair_modify mix arithmetic\n");
|
printf(LAMMPS "pair_modify mix arithmetic\n");
|
||||||
printf(LAMMPS "kspace_style pppm 1e-6\n\n");
|
printf(LAMMPS "kspace_style pppm 1e-6\n\n");
|
||||||
|
|
||||||
if ($cmap) {
|
if ($cmap) {
|
||||||
printf(LAMMPS "# Modify following line to point to the desired CMAP file\n");
|
printf(LAMMPS "# Modify following line to point to the desired CMAP file\n");
|
||||||
printf(LAMMPS "fix cmap all cmap charmm$cmap.cmap\n");
|
printf(LAMMPS "fix cmap all cmap charmm$cmap.cmap\n");
|
||||||
@ -1508,7 +1508,7 @@
|
|||||||
# Molecular Dynamics Simulations, J. Comput. Chem. 25(2004): 1400-1415. #
|
# Molecular Dynamics Simulations, J. Comput. Chem. 25(2004): 1400-1415. #
|
||||||
# ---------------------------------------------------------------------------- #
|
# ---------------------------------------------------------------------------- #
|
||||||
|
|
||||||
sub CharmmCmap
|
sub CharmmCmap
|
||||||
{
|
{
|
||||||
print "\nINITIATING CHARMM CMAP SUBROUTINE...\n\n";
|
print "\nINITIATING CHARMM CMAP SUBROUTINE...\n\n";
|
||||||
|
|
||||||
@ -1664,7 +1664,7 @@
|
|||||||
# ...
|
# ...
|
||||||
#
|
#
|
||||||
# Criteria to be a PHI/PSI dihedral pair:
|
# Criteria to be a PHI/PSI dihedral pair:
|
||||||
# 1. Atoms have to match with the mass/charge constellations as
|
# 1. Atoms have to match with the mass/charge constellations as
|
||||||
# defined above.
|
# defined above.
|
||||||
# 2. The atoms N--CA--C needs to be covalently bonded with each
|
# 2. The atoms N--CA--C needs to be covalently bonded with each
|
||||||
# other.
|
# other.
|
||||||
@ -1734,7 +1734,7 @@
|
|||||||
my $N_PRO_counter = 0;
|
my $N_PRO_counter = 0;
|
||||||
|
|
||||||
my $C_flag = 0;
|
my $C_flag = 0;
|
||||||
|
|
||||||
for (my $i = 0; $i <= $natom_number; $i++) {
|
for (my $i = 0; $i <= $natom_number; $i++) {
|
||||||
my $cur_type = ${$atoms_matrix[$i]}[2];
|
my $cur_type = ${$atoms_matrix[$i]}[2];
|
||||||
my $cur_charge = ${$atoms_matrix[$i]}[3];
|
my $cur_charge = ${$atoms_matrix[$i]}[3];
|
||||||
@ -1777,8 +1777,8 @@
|
|||||||
}
|
}
|
||||||
|
|
||||||
# Quit if one of the atom types dosen't exist
|
# Quit if one of the atom types dosen't exist
|
||||||
if ( $C_counter == 0 or
|
if ( $C_counter == 0 or
|
||||||
($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) or
|
($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) or
|
||||||
($N_counter == 0 and $N_PRO_counter == 0) ) {
|
($N_counter == 0 and $N_PRO_counter == 0) ) {
|
||||||
if ($C_counter == 0) {
|
if ($C_counter == 0) {
|
||||||
print "\nCannot find the peptide backbone C atom type\n";
|
print "\nCannot find the peptide backbone C atom type\n";
|
||||||
@ -1814,21 +1814,21 @@
|
|||||||
my $cur_atom4_type = ${atoms_matrix[${dihedrals_matrix[$i]}[5]-1]}[2];
|
my $cur_atom4_type = ${atoms_matrix[${dihedrals_matrix[$i]}[5]-1]}[2];
|
||||||
|
|
||||||
next if (${dihedrals_matrix[$i]}[2] == ${dihedrals_matrix[$i-1]}[2] and
|
next if (${dihedrals_matrix[$i]}[2] == ${dihedrals_matrix[$i-1]}[2] and
|
||||||
${dihedrals_matrix[$i]}[3] == ${dihedrals_matrix[$i-1]}[3] and
|
${dihedrals_matrix[$i]}[3] == ${dihedrals_matrix[$i-1]}[3] and
|
||||||
${dihedrals_matrix[$i]}[4] == ${dihedrals_matrix[$i-1]}[4] and
|
${dihedrals_matrix[$i]}[4] == ${dihedrals_matrix[$i-1]}[4] and
|
||||||
${dihedrals_matrix[$i]}[5] == ${dihedrals_matrix[$i-1]}[5]);
|
${dihedrals_matrix[$i]}[5] == ${dihedrals_matrix[$i-1]}[5]);
|
||||||
|
|
||||||
# Determine PHI-dihedrals; If C-CA-N-C or C-N-CA-C, then save it in a list
|
# Determine PHI-dihedrals; If C-CA-N-C or C-N-CA-C, then save it in a list
|
||||||
if ($cur_atom1_type == $C_type and $cur_atom4_type == $C_type) {
|
if ($cur_atom1_type == $C_type and $cur_atom4_type == $C_type) {
|
||||||
if ( ( ($cur_atom2_type == $CA_type or
|
if ( ( ($cur_atom2_type == $CA_type or
|
||||||
$cur_atom2_type == $CA_GLY_type or
|
$cur_atom2_type == $CA_GLY_type or
|
||||||
$cur_atom2_type == $CA_PRO_type) and
|
$cur_atom2_type == $CA_PRO_type) and
|
||||||
($cur_atom3_type == $N_type or
|
($cur_atom3_type == $N_type or
|
||||||
$cur_atom3_type == $N_PRO_type) ) or
|
$cur_atom3_type == $N_PRO_type) ) or
|
||||||
( ($cur_atom3_type == $CA_type or
|
( ($cur_atom3_type == $CA_type or
|
||||||
$cur_atom3_type == $CA_GLY_type or
|
$cur_atom3_type == $CA_GLY_type or
|
||||||
$cur_atom3_type == $CA_PRO_type) and
|
$cur_atom3_type == $CA_PRO_type) and
|
||||||
($cur_atom2_type == $N_type or
|
($cur_atom2_type == $N_type or
|
||||||
$cur_atom2_type == $N_PRO_type) ) ) {
|
$cur_atom2_type == $N_PRO_type) ) ) {
|
||||||
push (@PHI_dihedrals,$cur_dihe_ID);
|
push (@PHI_dihedrals,$cur_dihe_ID);
|
||||||
$PHI_counter++;
|
$PHI_counter++;
|
||||||
@ -1837,17 +1837,17 @@
|
|||||||
|
|
||||||
# Determin PSI-dihedrals; If N-CA-C-N or N-C-CA-N (N can be both normal N or N proline),
|
# Determin PSI-dihedrals; If N-CA-C-N or N-C-CA-N (N can be both normal N or N proline),
|
||||||
# then save it in a list
|
# then save it in a list
|
||||||
if ( ($cur_atom1_type == $N_type and $cur_atom4_type == $N_type) or
|
if ( ($cur_atom1_type == $N_type and $cur_atom4_type == $N_type) or
|
||||||
($cur_atom4_type == $N_PRO_type and $cur_atom1_type == $N_PRO_type) or
|
($cur_atom4_type == $N_PRO_type and $cur_atom1_type == $N_PRO_type) or
|
||||||
($cur_atom1_type == $N_type and $cur_atom4_type == $N_PRO_type) or
|
($cur_atom1_type == $N_type and $cur_atom4_type == $N_PRO_type) or
|
||||||
($cur_atom4_type == $N_type and $cur_atom1_type == $N_PRO_type) ) {
|
($cur_atom4_type == $N_type and $cur_atom1_type == $N_PRO_type) ) {
|
||||||
if ( ( ($cur_atom2_type == $CA_type or
|
if ( ( ($cur_atom2_type == $CA_type or
|
||||||
$cur_atom2_type == $CA_GLY_type or
|
$cur_atom2_type == $CA_GLY_type or
|
||||||
$cur_atom2_type == $CA_PRO_type) and
|
$cur_atom2_type == $CA_PRO_type) and
|
||||||
$cur_atom3_type == $C_type) or
|
$cur_atom3_type == $C_type) or
|
||||||
( ($cur_atom3_type == $CA_type or
|
( ($cur_atom3_type == $CA_type or
|
||||||
$cur_atom3_type == $CA_GLY_type or
|
$cur_atom3_type == $CA_GLY_type or
|
||||||
$cur_atom3_type == $CA_PRO_type) and
|
$cur_atom3_type == $CA_PRO_type) and
|
||||||
$cur_atom2_type == $C_type) ) {
|
$cur_atom2_type == $C_type) ) {
|
||||||
push (@PSI_dihedrals,$cur_dihe_ID);
|
push (@PSI_dihedrals,$cur_dihe_ID);
|
||||||
$PSI_counter++;
|
$PSI_counter++;
|
||||||
@ -1871,7 +1871,7 @@
|
|||||||
#
|
#
|
||||||
# The algorithm:
|
# The algorithm:
|
||||||
# _____
|
# _____
|
||||||
# | |
|
# | |
|
||||||
# 1--2--3--4 PHI-dihedral
|
# 1--2--3--4 PHI-dihedral
|
||||||
# 4--3--2--1
|
# 4--3--2--1
|
||||||
# --C--N-CA--C--N-- Peptide backbone
|
# --C--N-CA--C--N-- Peptide backbone
|
||||||
@ -1887,7 +1887,7 @@
|
|||||||
# if (2--3--4) = (4--3--2)
|
# if (2--3--4) = (4--3--2)
|
||||||
# or
|
# or
|
||||||
# if (3--2--1) = (1--2--3)
|
# if (3--2--1) = (1--2--3)
|
||||||
# or
|
# or
|
||||||
# if (3--2--1) = (4--3--2),
|
# if (3--2--1) = (4--3--2),
|
||||||
#
|
#
|
||||||
# then these 2 dihedrals are a PHI/PSI pair. If a pair is found, the
|
# then these 2 dihedrals are a PHI/PSI pair. If a pair is found, the
|
||||||
@ -1940,7 +1940,7 @@
|
|||||||
|
|
||||||
if ($crossterm_CA_charge == $charge_CA) { $crossterm_type = 1; $crossterm_type1_flag = 1; }
|
if ($crossterm_CA_charge == $charge_CA) { $crossterm_type = 1; $crossterm_type1_flag = 1; }
|
||||||
if ($crossterm_CA_charge == $charge_CA_GLY) { $crossterm_type = 5; $crossterm_type5_flag = 1; }
|
if ($crossterm_CA_charge == $charge_CA_GLY) { $crossterm_type = 5; $crossterm_type5_flag = 1; }
|
||||||
if ($crossterm_CA_charge == $charge_CA_PRO) {
|
if ($crossterm_CA_charge == $charge_CA_PRO) {
|
||||||
$crossterm_type = 3; $crossterm_type3_flag = 1;
|
$crossterm_type = 3; $crossterm_type3_flag = 1;
|
||||||
# Checking the last crossterm, re-assign the last crossterm type if needed
|
# Checking the last crossterm, re-assign the last crossterm type if needed
|
||||||
if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 1) {
|
if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 1) {
|
||||||
@ -1998,7 +1998,7 @@
|
|||||||
print "acid abbreviation for that amino acid, and <#2> is the molecule number\n";
|
print "acid abbreviation for that amino acid, and <#2> is the molecule number\n";
|
||||||
print "of the terminal amino acid residue.\n\n";
|
print "of the terminal amino acid residue.\n\n";
|
||||||
print "For example, if the last atom of the last amino acid in the peptide\n";
|
print "For example, if the last atom of the last amino acid in the peptide\n";
|
||||||
print "sequence is listed in the pdb file as:\n\n";
|
print "sequence is listed in the pdb file as:\n\n";
|
||||||
print " 'ATOM 853 O GLU P 56 12.089 -1.695 -6.543 1.00 1.03 PROA'\n\n";
|
print " 'ATOM 853 O GLU P 56 12.089 -1.695 -6.543 1.00 1.03 PROA'\n\n";
|
||||||
print "you would insert the following line after it:\n\n";
|
print "you would insert the following line after it:\n\n";
|
||||||
print " 'TER 854 GLU 56'\n\n";
|
print " 'TER 854 GLU 56'\n\n";
|
||||||
@ -2016,7 +2016,7 @@
|
|||||||
# Print out PHI/PSI diheral pair list
|
# Print out PHI/PSI diheral pair list
|
||||||
my $pair_counter = 0;
|
my $pair_counter = 0;
|
||||||
# Don't presently use $ncrosstermtypes but have this available if wish to print it out
|
# Don't presently use $ncrosstermtypes but have this available if wish to print it out
|
||||||
my $ncrosstermtypes = $crossterm_type1_flag + $crossterm_type2_flag + $crossterm_type3_flag +
|
my $ncrosstermtypes = $crossterm_type1_flag + $crossterm_type2_flag + $crossterm_type3_flag +
|
||||||
$crossterm_type4_flag + $crossterm_type5_flag + $crossterm_type6_flag;
|
$crossterm_type4_flag + $crossterm_type5_flag + $crossterm_type6_flag;
|
||||||
print "\nWriting \"$project.data\" with section \"CMAP crossterms\" added at the end.\n";
|
print "\nWriting \"$project.data\" with section \"CMAP crossterms\" added at the end.\n";
|
||||||
|
|
||||||
|
|||||||
@ -8,9 +8,9 @@
|
|||||||
# conjunction with vmd
|
# conjunction with vmd
|
||||||
#
|
#
|
||||||
# Notes: Copyright by author for Sandia National Laboratories
|
# Notes: Copyright by author for Sandia National Laboratories
|
||||||
# 20040903 Conception date of v1.0: rudimentary script for collagen
|
# 20040903 Conception date of v1.0: rudimentary script for collagen
|
||||||
# project.
|
# project.
|
||||||
# 20050423 Conception date of v2.0:
|
# 20050423 Conception date of v2.0:
|
||||||
# - changed data access through indexing data directly on disk;
|
# - changed data access through indexing data directly on disk;
|
||||||
# - added all command line options
|
# - added all command line options
|
||||||
# 20050425 Corrected focussing to use a target molecule's moment of
|
# 20050425 Corrected focussing to use a target molecule's moment of
|
||||||
@ -22,21 +22,21 @@
|
|||||||
# the data stream.
|
# the data stream.
|
||||||
|
|
||||||
# subroutines
|
# subroutines
|
||||||
|
|
||||||
sub test
|
sub test
|
||||||
{
|
{
|
||||||
my $name = shift(@_);
|
my $name = shift(@_);
|
||||||
|
|
||||||
printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
|
printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
|
||||||
return !scalar(stat($name));
|
return !scalar(stat($name));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub initialize
|
sub initialize
|
||||||
{
|
{
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
my @options = ("-help", "-nstart", "-dn", "-cut", "-repair",
|
my @options = ("-help", "-nstart", "-dn", "-cut", "-repair",
|
||||||
"-units", "-quiet", "-nodetect", "-data", "-pbc",
|
"-units", "-quiet", "-nodetect", "-data", "-pbc",
|
||||||
"-focus", "-center", "-exclude");
|
"-focus", "-center", "-exclude");
|
||||||
my @remarks = ("display this message",
|
my @remarks = ("display this message",
|
||||||
"starting frame [-1]",
|
"starting frame [-1]",
|
||||||
@ -61,7 +61,7 @@
|
|||||||
"* Expected files in current directory: project.data, project.dump",
|
"* Expected files in current directory: project.data, project.dump",
|
||||||
"* Generated output files: project_trj.psf, project_trj.pdb",
|
"* Generated output files: project_trj.psf, project_trj.pdb",
|
||||||
"* Uses project_ctrl.psf if available");
|
"* Uses project_ctrl.psf if available");
|
||||||
|
|
||||||
|
|
||||||
$program = "lammps2pdb";
|
$program = "lammps2pdb";
|
||||||
$version = "2.2.5";
|
$version = "2.2.5";
|
||||||
@ -96,7 +96,7 @@
|
|||||||
$info = $switch ? 0 : 1 if (!$k--);
|
$info = $switch ? 0 : 1 if (!$k--);
|
||||||
$detect = $switch ? 0 : 1 if (!$k--);
|
$detect = $switch ? 0 : 1 if (!$k--);
|
||||||
$data_name = $arg[1] if (!$k--);
|
$data_name = $arg[1] if (!$k--);
|
||||||
if (!$k--) {
|
if (!$k--) {
|
||||||
if ($switch) { $pbc{ALL} = 1; }
|
if ($switch) { $pbc{ALL} = 1; }
|
||||||
else { foreach (split(",",$arg[1])) { $pbc{uc($_)} = 1; }}}
|
else { foreach (split(",",$arg[1])) { $pbc{uc($_)} = 1; }}}
|
||||||
if (!$k--) { foreach (split(",",$arg[1])) { $focus{uc($_)} = uc($_);}}
|
if (!$k--) { foreach (split(",",$arg[1])) { $focus{uc($_)} = uc($_);}}
|
||||||
@ -120,7 +120,7 @@
|
|||||||
printf("\n");
|
printf("\n");
|
||||||
exit(-1);
|
exit(-1);
|
||||||
}
|
}
|
||||||
printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info);
|
printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info);
|
||||||
|
|
||||||
$data_name = $project.".data" if ($data_name eq "");
|
$data_name = $project.".data" if ($data_name eq "");
|
||||||
$traject_name = $project.".dump";
|
$traject_name = $project.".dump";
|
||||||
@ -133,7 +133,7 @@
|
|||||||
my $flag = test($data_name);
|
my $flag = test($data_name);
|
||||||
printf("Conversion aborted\n\n") if ($flag);
|
printf("Conversion aborted\n\n") if ($flag);
|
||||||
exit(-1) if ($flag);
|
exit(-1) if ($flag);
|
||||||
|
|
||||||
# data input
|
# data input
|
||||||
|
|
||||||
create_atom_ids();
|
create_atom_ids();
|
||||||
@ -145,9 +145,9 @@
|
|||||||
|
|
||||||
open(PSF, ">".$psf_name) if (!$psf_ctrl);
|
open(PSF, ">".$psf_name) if (!$psf_ctrl);
|
||||||
open(PDB, ">".$pdb_name);
|
open(PDB, ">".$pdb_name);
|
||||||
|
|
||||||
# align center with focus
|
# align center with focus
|
||||||
|
|
||||||
%center = %focus if (scalar(%focus));
|
%center = %focus if (scalar(%focus));
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -166,24 +166,24 @@
|
|||||||
return @_;
|
return @_;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Add # V_Add(@a, @b) = @a + @b;
|
sub V_Add # V_Add(@a, @b) = @a + @b;
|
||||||
{
|
{
|
||||||
return (@_[0]+@_[3], @_[1]+@_[4], @_[2]+@_[5]);
|
return (@_[0]+@_[3], @_[1]+@_[4], @_[2]+@_[5]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Subtr # V_Subtr(@a, @b) = @a - @b;
|
sub V_Subtr # V_Subtr(@a, @b) = @a - @b;
|
||||||
{
|
{
|
||||||
return (@_[0]-@_[3], @_[1]-@_[4], @_[2]-@_[5]);
|
return (@_[0]-@_[3], @_[1]-@_[4], @_[2]-@_[5]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Dot # V_Dot(@a, @b) = @a . @b;
|
sub V_Dot # V_Dot(@a, @b) = @a . @b;
|
||||||
{
|
{
|
||||||
return (@_[0]*@_[3]+@_[1]*@_[4]+@_[2]*@_[5]);
|
return (@_[0]*@_[3]+@_[1]*@_[4]+@_[2]*@_[5]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Cross # V_Cross(@a, @b) = @a x @b;
|
sub V_Cross # V_Cross(@a, @b) = @a x @b;
|
||||||
{
|
{
|
||||||
@ -191,7 +191,7 @@
|
|||||||
@_[0]*@_[4]-@_[1]*@_[3]);
|
@_[0]*@_[4]-@_[1]*@_[3]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Mult # V_Mult($f, @a) = $f * @a;
|
sub V_Mult # V_Mult($f, @a) = $f * @a;
|
||||||
{
|
{
|
||||||
return (@_[0]*@_[1], @_[0]*@_[2], @_[0]*@_[3]);
|
return (@_[0]*@_[1], @_[0]*@_[2], @_[0]*@_[3]);
|
||||||
@ -203,11 +203,11 @@
|
|||||||
return V_Mult(1/sqrt(V_Dot(@_[0,1,2],@_[0,1,2])), @_[0,1,2]);
|
return V_Mult(1/sqrt(V_Dot(@_[0,1,2],@_[0,1,2])), @_[0,1,2]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pbc # periodic -0.5*L <= x < 0.5*L
|
sub pbc # periodic -0.5*L <= x < 0.5*L
|
||||||
{
|
{
|
||||||
my $x = @_[0]/@_[1]+0.5;
|
my $x = @_[0]/@_[1]+0.5;
|
||||||
|
|
||||||
return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));
|
return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -216,8 +216,8 @@
|
|||||||
{
|
{
|
||||||
return (pbc(@_[0], @_[3]), pbc(@_[1], @_[4]), pbc(@_[2], @_[5]));
|
return (pbc(@_[0], @_[3]), pbc(@_[1], @_[4]), pbc(@_[2], @_[5]));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Cmp # V_Cmp(abs(@a), abs(@b))
|
sub V_Cmp # V_Cmp(abs(@a), abs(@b))
|
||||||
{
|
{
|
||||||
return -1 if (abs($_[0])<abs($_[3]));
|
return -1 if (abs($_[0])<abs($_[3]));
|
||||||
@ -228,12 +228,12 @@
|
|||||||
return 1 if (abs($_[2])>abs($_[5]));
|
return 1 if (abs($_[2])>abs($_[5]));
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub V_Sort # sort on descending absolute
|
sub V_Sort # sort on descending absolute
|
||||||
{ # value
|
{ # value
|
||||||
my @v = @_;
|
my @v = @_;
|
||||||
|
|
||||||
for (my $i=0; $i<scalar(@v)-3; $i+=3)
|
for (my $i=0; $i<scalar(@v)-3; $i+=3)
|
||||||
{
|
{
|
||||||
for (my $j=$i+3; $j<scalar(@v); $j+=3)
|
for (my $j=$i+3; $j<scalar(@v); $j+=3)
|
||||||
@ -247,13 +247,13 @@
|
|||||||
return @v;
|
return @v;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
# Matrix routines
|
# Matrix routines
|
||||||
|
|
||||||
sub M_String # M_String(@A)
|
sub M_String # M_String(@A)
|
||||||
{
|
{
|
||||||
my @M;
|
my @M;
|
||||||
|
|
||||||
for (my $i=0; $i<3; ++$i) { push(@M, V_String(splice(@_, 0, 3))); }
|
for (my $i=0; $i<3; ++$i) { push(@M, V_String(splice(@_, 0, 3))); }
|
||||||
return "{".join(", ", @M)."}";
|
return "{".join(", ", @M)."}";
|
||||||
}
|
}
|
||||||
@ -270,7 +270,7 @@
|
|||||||
return (@_[0], @_[3], @_[6], @_[1], @_[4], @_[7], @_[2], @_[5], @_[8]);
|
return (@_[0], @_[3], @_[6], @_[1], @_[4], @_[7], @_[2], @_[5], @_[8]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub M_Dot # M_Dot(@A, @B) = @A . @B;
|
sub M_Dot # M_Dot(@A, @B) = @A . @B;
|
||||||
{
|
{
|
||||||
return (
|
return (
|
||||||
@ -288,7 +288,7 @@
|
|||||||
return V_Dot(@_[0,1,2], V_Cross(@_[3,4,5], @_[6,7,8]));
|
return V_Dot(@_[0,1,2], V_Cross(@_[3,4,5], @_[6,7,8]));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub M_Mult # M_Mult($a, @A) = $a * @A
|
sub M_Mult # M_Mult($a, @A) = $a * @A
|
||||||
{
|
{
|
||||||
return (
|
return (
|
||||||
@ -296,12 +296,12 @@
|
|||||||
@_[0]*@_[4], @_[0]*@_[5], @_[0]*@_[6],
|
@_[0]*@_[4], @_[0]*@_[5], @_[0]*@_[6],
|
||||||
@_[0]*@_[7], @_[0]*@_[8], @_[0]*@_[9]);
|
@_[0]*@_[7], @_[0]*@_[8], @_[0]*@_[9]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
|
sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
|
||||||
|
|
||||||
sub PI { return 4*atan2(1,1); }
|
sub PI { return 4*atan2(1,1); }
|
||||||
|
|
||||||
sub M_Rotate # M_Rotate($n, $alpha) = @R_$n;
|
sub M_Rotate # M_Rotate($n, $alpha) = @R_$n;
|
||||||
{ # vmd convention
|
{ # vmd convention
|
||||||
my $n = shift(@_);
|
my $n = shift(@_);
|
||||||
@ -316,7 +316,7 @@
|
|||||||
return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
|
return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
|
||||||
return M_Unit();
|
return M_Unit();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub M_RotateNormal # returns R.(1,0,0) = @a/|@a|;
|
sub M_RotateNormal # returns R.(1,0,0) = @a/|@a|;
|
||||||
{
|
{
|
||||||
@ -324,7 +324,7 @@
|
|||||||
my @n = V_Mult(1.0/sqrt(V_Dot(@_[0,1,2], @_)), @_);
|
my @n = V_Mult(1.0/sqrt(V_Dot(@_[0,1,2], @_)), @_);
|
||||||
my $sina = $n[1]<0 ? -sqrt($n[1]*$n[1]+$n[2]*$n[2]) :
|
my $sina = $n[1]<0 ? -sqrt($n[1]*$n[1]+$n[2]*$n[2]) :
|
||||||
sqrt($n[1]*$n[1]+$n[2]*$n[2]);
|
sqrt($n[1]*$n[1]+$n[2]*$n[2]);
|
||||||
|
|
||||||
if ($sina)
|
if ($sina)
|
||||||
{
|
{
|
||||||
my $cosa = $n[0];
|
my $cosa = $n[0];
|
||||||
@ -337,8 +337,8 @@
|
|||||||
}
|
}
|
||||||
return @R;
|
return @R;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub MV_Dot # MV_Dot(@A, @b) = @A . @b;
|
sub MV_Dot # MV_Dot(@A, @b) = @A . @b;
|
||||||
{
|
{
|
||||||
return (V_Dot(@_[0,1,2], @_[9,10,11]), V_Dot(@_[3,4,5], @_[9,10,11]),
|
return (V_Dot(@_[0,1,2], @_[9,10,11]), V_Dot(@_[3,4,5], @_[9,10,11]),
|
||||||
@ -374,14 +374,14 @@
|
|||||||
{
|
{
|
||||||
return (@_[0]+@_[2], @_[1]+@_[3]);
|
return (@_[0]+@_[2], @_[1]+@_[3]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub C_Subtr # z = z1 - z2
|
sub C_Subtr # z = z1 - z2
|
||||||
{
|
{
|
||||||
return (@_[0]-@_[2], @_[1]-@_[3]);
|
return (@_[0]-@_[2], @_[1]-@_[3]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub C_Mult # z = z1 * z2
|
sub C_Mult # z = z1 * z2
|
||||||
{
|
{
|
||||||
return (@_[0]*@_[2]-@_[1]*@_[3], @_[0]*@_[3]+@_[2]*@_[1]);
|
return (@_[0]*@_[2]-@_[1]*@_[3], @_[0]*@_[3]+@_[2]*@_[1]);
|
||||||
@ -404,7 +404,7 @@
|
|||||||
return ($r*cos($a), $r*sin($a));
|
return ($r*cos($a), $r*sin($a));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub C_Correct
|
sub C_Correct
|
||||||
{
|
{
|
||||||
return (abs(@_[0])<1e-14 ? 0 : @_[0], abs(@_[1])<1e-14 ? 0 : @_[1]);
|
return (abs(@_[0])<1e-14 ? 0 : @_[0], abs(@_[1])<1e-14 ? 0 : @_[1]);
|
||||||
@ -422,7 +422,7 @@
|
|||||||
return (@_[0], -@_[1]);
|
return (@_[0], -@_[1]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub C_String
|
sub C_String
|
||||||
{
|
{
|
||||||
return @_[0]." + ".@_[1]."i";
|
return @_[0]." + ".@_[1]."i";
|
||||||
@ -434,12 +434,12 @@
|
|||||||
sub R_Sort
|
sub R_Sort
|
||||||
{
|
{
|
||||||
my $n = scalar(@_);
|
my $n = scalar(@_);
|
||||||
|
|
||||||
for (my $i=0; $i<$n-2; $i+=2)
|
for (my $i=0; $i<$n-2; $i+=2)
|
||||||
{
|
{
|
||||||
for (my $j=$i+2; $j<$n; $j+=2)
|
for (my $j=$i+2; $j<$n; $j+=2)
|
||||||
{
|
{
|
||||||
if (@_[$j]<@_[$i]) {
|
if (@_[$j]<@_[$i]) {
|
||||||
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; }
|
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; }
|
||||||
else { if ((@_[$j]==@_[$i])&&(@_[$j+1]<@_[$i+1])) {
|
else { if ((@_[$j]==@_[$i])&&(@_[$j+1]<@_[$i+1])) {
|
||||||
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; } }
|
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; } }
|
||||||
@ -448,7 +448,7 @@
|
|||||||
return @_;
|
return @_;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub R_First
|
sub R_First
|
||||||
{
|
{
|
||||||
return (0, 0) if (abs(@_[1])<1e-14);
|
return (0, 0) if (abs(@_[1])<1e-14);
|
||||||
@ -476,16 +476,16 @@
|
|||||||
my @B = (0, 0);
|
my @B = (0, 0);
|
||||||
my @z1 = (0.5, 0.5*sqrt(3));
|
my @z1 = (0.5, 0.5*sqrt(3));
|
||||||
my @z2 = C_Conj(@z1);
|
my @z2 = C_Conj(@z1);
|
||||||
|
|
||||||
if (abs($f1)<1e-3) { # limit f1 -> 0
|
if (abs($f1)<1e-3) { # limit f1 -> 0
|
||||||
@A = ($f2<0 ? abs(2*$f2)**(1/3) : 0, 0); }
|
@A = ($f2<0 ? abs(2*$f2)**(1/3) : 0, 0); }
|
||||||
else {
|
else {
|
||||||
if (abs($f2)<1e-14) { # limit f2 -> 0
|
if (abs($f2)<1e-14) { # limit f2 -> 0
|
||||||
my $f = sqrt(abs($f1))/$c3;
|
my $f = sqrt(abs($f1))/$c3;
|
||||||
@A = $f1<0 ? (-$f*$z1[1], 0.5*$f) : ($f, 0);
|
@A = $f1<0 ? (-$f*$z1[1], 0.5*$f) : ($f, 0);
|
||||||
@B = $f1<0 ? (-$A[0], $A[1]) : ($f, 0); }
|
@B = $f1<0 ? (-$A[0], $A[1]) : ($f, 0); }
|
||||||
else {
|
else {
|
||||||
@B = C_Pow(C_Add(($f2, 0),
|
@B = C_Pow(C_Add(($f2, 0),
|
||||||
C_Pow(($f1*$f1*$f1+$f2*$f2, 0), 1/2)), 1/3);
|
C_Pow(($f1*$f1*$f1+$f2*$f2, 0), 1/2)), 1/3);
|
||||||
@A = C_Div(($f1/$c3, 0), @B);
|
@A = C_Div(($f1/$c3, 0), @B);
|
||||||
@B = ($B[0]/$c3, $B[1]/$c3); } }
|
@B = ($B[0]/$c3, $B[1]/$c3); } }
|
||||||
@ -503,21 +503,21 @@
|
|||||||
my $input = shift;
|
my $input = shift;
|
||||||
my $dlines = shift;
|
my $dlines = shift;
|
||||||
my $read;
|
my $read;
|
||||||
|
|
||||||
while ($dlines--) { $read = <$input>; }
|
while ($dlines--) { $read = <$input>; }
|
||||||
return $read;
|
return $read;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub rewind_read
|
sub rewind_read
|
||||||
{
|
{
|
||||||
my $input = shift;
|
my $input = shift;
|
||||||
|
|
||||||
seek($input, 0, SEEK_SET);
|
seek($input, 0, SEEK_SET);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
# create crossreference tables
|
# create crossreference tables
|
||||||
|
|
||||||
sub create_psf_index # make an index of id
|
sub create_psf_index # make an index of id
|
||||||
{ # locations
|
{ # locations
|
||||||
@ -538,13 +538,13 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub psf_goto # goto $ident in <PSF>
|
sub psf_goto # goto $ident in <PSF>
|
||||||
{
|
{
|
||||||
create_psf_index() if (!scalar(%PSFIndex));
|
create_psf_index() if (!scalar(%PSFIndex));
|
||||||
my $id = shift(@_);
|
my $id = shift(@_);
|
||||||
my @n = split(" ", $PSFIndex{$id});
|
my @n = split(" ", $PSFIndex{$id});
|
||||||
|
|
||||||
@PSFBuffer = ();
|
@PSFBuffer = ();
|
||||||
if (!scalar(@n))
|
if (!scalar(@n))
|
||||||
{
|
{
|
||||||
@ -571,7 +571,7 @@
|
|||||||
my $id;
|
my $id;
|
||||||
my %hash;
|
my %hash;
|
||||||
my %size;
|
my %size;
|
||||||
|
|
||||||
foreach ((masses,atoms,bonds,angles,dihedrals,impropers)) { $hash{$_}=$_; }
|
foreach ((masses,atoms,bonds,angles,dihedrals,impropers)) { $hash{$_}=$_; }
|
||||||
open(DATA, "<".$data_name);
|
open(DATA, "<".$data_name);
|
||||||
for (my $i=0; $i<2; ++$i) { my $tmp = <DATA>; } # skip first two lines
|
for (my $i=0; $i<2; ++$i) { my $tmp = <DATA>; } # skip first two lines
|
||||||
@ -604,7 +604,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub goto_data
|
sub goto_data
|
||||||
{
|
{
|
||||||
create_data_index() if (!scalar(%DATAIndex));
|
create_data_index() if (!scalar(%DATAIndex));
|
||||||
@ -623,7 +623,7 @@
|
|||||||
|
|
||||||
|
|
||||||
# create atom and residue identifiers
|
# create atom and residue identifiers
|
||||||
|
|
||||||
sub create_names
|
sub create_names
|
||||||
{
|
{
|
||||||
return if (scalar(@names));
|
return if (scalar(@names));
|
||||||
@ -636,7 +636,7 @@
|
|||||||
my @letter = ("X", "Y", "Z", "P", "Q", "R", "S", "A", "B", "C");
|
my @letter = ("X", "Y", "Z", "P", "Q", "R", "S", "A", "B", "C");
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
my %atom;
|
my %atom;
|
||||||
|
|
||||||
$names[0] = "";
|
$names[0] = "";
|
||||||
foreach (@mass) { $atom{$_} = shift(@name); }
|
foreach (@mass) { $atom{$_} = shift(@name); }
|
||||||
for (my $i=1; $i<=$n; ++$i)
|
for (my $i=1; $i<=$n; ++$i)
|
||||||
@ -658,7 +658,7 @@
|
|||||||
my @data = @_;
|
my @data = @_;
|
||||||
my $p = $data[1]." ".$data[2];
|
my $p = $data[1]." ".$data[2];
|
||||||
my $k;
|
my $k;
|
||||||
|
|
||||||
for ($k=0; ($k<scalar(@data))&&(substr($data[$k],0,1) ne "#"); ++$k) { }
|
for ($k=0; ($k<scalar(@data))&&(substr($data[$k],0,1) ne "#"); ++$k) { }
|
||||||
@data = splice(@data, $k-($k<8 ? 3 : 6), $k<8 ? 3 : 6);
|
@data = splice(@data, $k-($k<8 ? 3 : 6), $k<8 ? 3 : 6);
|
||||||
foreach (@L)
|
foreach (@L)
|
||||||
@ -669,8 +669,8 @@
|
|||||||
}
|
}
|
||||||
return $p;
|
return $p;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub create_atom_ids
|
sub create_atom_ids
|
||||||
{
|
{
|
||||||
my $res = 0;
|
my $res = 0;
|
||||||
@ -682,7 +682,7 @@
|
|||||||
my $id;
|
my $id;
|
||||||
my %link;
|
my %link;
|
||||||
my %special;
|
my %special;
|
||||||
|
|
||||||
printf("Info: creating atom ids\n") if ($info);
|
printf("Info: creating atom ids\n") if ($info);
|
||||||
create_names();
|
create_names();
|
||||||
$n = goto_data(atoms);
|
$n = goto_data(atoms);
|
||||||
@ -696,8 +696,8 @@
|
|||||||
{
|
{
|
||||||
if ((($tmp = $link{$id = join(" ", sort(split(" ", $id)))}) eq "")&&
|
if ((($tmp = $link{$id = join(" ", sort(split(" ", $id)))}) eq "")&&
|
||||||
(($tmp = $special{$id}) eq ""))
|
(($tmp = $special{$id}) eq ""))
|
||||||
{
|
{
|
||||||
$link{$id} =
|
$link{$id} =
|
||||||
$tmp = "R".($res<10 ? "0" : "").$res;
|
$tmp = "R".($res<10 ? "0" : "").$res;
|
||||||
++$res;
|
++$res;
|
||||||
}
|
}
|
||||||
@ -712,12 +712,12 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub crossover
|
sub crossover
|
||||||
{
|
{
|
||||||
my @d = V_Subtr((split(" ", $position[@_[0]]))[0,1,2],
|
my @d = V_Subtr((split(" ", $position[@_[0]]))[0,1,2],
|
||||||
(split(" ", $position[@_[1]]))[0,1,2]);
|
(split(" ", $position[@_[1]]))[0,1,2]);
|
||||||
|
|
||||||
$d[0] /= $l[3];
|
$d[0] /= $l[3];
|
||||||
$d[1] /= $l[4];
|
$d[1] /= $l[4];
|
||||||
$d[2] /= $l[5];
|
$d[2] /= $l[5];
|
||||||
@ -744,7 +744,7 @@
|
|||||||
{
|
{
|
||||||
my $n = scalar(@bonds);
|
my $n = scalar(@bonds);
|
||||||
my $i = 0;
|
my $i = 0;
|
||||||
|
|
||||||
printf("Info: deleting excluded bonds\n") if ($info);
|
printf("Info: deleting excluded bonds\n") if ($info);
|
||||||
while ($i<$n)
|
while ($i<$n)
|
||||||
{
|
{
|
||||||
@ -754,12 +754,12 @@
|
|||||||
else { ++$i; }
|
else { ++$i; }
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub create_bonds
|
sub create_bonds
|
||||||
{
|
{
|
||||||
my $n = goto_data(bonds);
|
my $n = goto_data(bonds);
|
||||||
|
|
||||||
printf("Info: creating bonds\n") if ($info);
|
printf("Info: creating bonds\n") if ($info);
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
@ -779,20 +779,20 @@
|
|||||||
while (!eof(TRAJECT)&&(substr(lc(join(" ", split(" ", <TRAJECT>))),
|
while (!eof(TRAJECT)&&(substr(lc(join(" ", split(" ", <TRAJECT>))),
|
||||||
0,length($subject)) ne $subject)) {}
|
0,length($subject)) ne $subject)) {}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub read_traject
|
sub read_traject
|
||||||
{
|
{
|
||||||
my @box;
|
my @box;
|
||||||
my @l;
|
my @l;
|
||||||
|
|
||||||
advance_traject("timestep");
|
advance_traject("timestep");
|
||||||
my $timestep = (split(" ", <TRAJECT>))[0];
|
my $timestep = (split(" ", <TRAJECT>))[0];
|
||||||
advance_traject("number of atoms");
|
advance_traject("number of atoms");
|
||||||
my $n = (split(" ", <TRAJECT>))[0];
|
my $n = (split(" ", <TRAJECT>))[0];
|
||||||
advance_traject("box bounds");
|
advance_traject("box bounds");
|
||||||
for (my $i=0; $i<3; ++$i)
|
for (my $i=0; $i<3; ++$i)
|
||||||
{
|
{
|
||||||
my @data = split(" ", <TRAJECT>);
|
my @data = split(" ", <TRAJECT>);
|
||||||
$box[$i] = $data[0]; # box edge
|
$box[$i] = $data[0]; # box edge
|
||||||
$l[$i] = $data[1]-$data[0]; # box length
|
$l[$i] = $data[1]-$data[0]; # box length
|
||||||
@ -806,9 +806,9 @@
|
|||||||
return ($timestep, $n, @box, @l);
|
return ($timestep, $n, @box, @l);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
# pdb format
|
# pdb format
|
||||||
|
|
||||||
sub eigen_vector # eigen_vector(@A, $l)
|
sub eigen_vector # eigen_vector(@A, $l)
|
||||||
{
|
{
|
||||||
my @A = splice(@_,0,9);
|
my @A = splice(@_,0,9);
|
||||||
@ -826,8 +826,8 @@
|
|||||||
return (0,0,1) if ($A[8]==1);
|
return (0,0,1) if ($A[8]==1);
|
||||||
return (0,0,0);
|
return (0,0,0);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_inertia
|
sub pdb_inertia
|
||||||
{
|
{
|
||||||
my @s = (
|
my @s = (
|
||||||
@ -852,13 +852,13 @@
|
|||||||
M_Transpose(M_RotateNormal(MV_Dot(@A,@b))));
|
M_Transpose(M_RotateNormal(MV_Dot(@A,@b))));
|
||||||
return M_Dot(@B, @A);
|
return M_Dot(@B, @A);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
sub pdb_focus # using moment of inertia
|
sub pdb_focus # using moment of inertia
|
||||||
{
|
{
|
||||||
my @R = pdb_inertia(@_);
|
my @R = pdb_inertia(@_);
|
||||||
|
|
||||||
printf("Info: focussing\n") if ($info);
|
printf("Info: focussing\n") if ($info);
|
||||||
foreach (@position)
|
foreach (@position)
|
||||||
{
|
{
|
||||||
@ -867,7 +867,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_center
|
sub pdb_center
|
||||||
{
|
{
|
||||||
my @c = splice(@_, 0, 3);
|
my @c = splice(@_, 0, 3);
|
||||||
@ -881,7 +881,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_pbc
|
sub pdb_pbc
|
||||||
{
|
{
|
||||||
printf("Info: applying periodicity\n") if ($info);
|
printf("Info: applying periodicity\n") if ($info);
|
||||||
@ -909,7 +909,7 @@
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_positions
|
sub pdb_positions
|
||||||
{
|
{
|
||||||
my @m = (0,0,0,0,0,0,0,0,0);
|
my @m = (0,0,0,0,0,0,0,0,0);
|
||||||
@ -918,7 +918,7 @@
|
|||||||
my $mass;
|
my $mass;
|
||||||
my @p;
|
my @p;
|
||||||
my $d;
|
my $d;
|
||||||
|
|
||||||
foreach (@traject)
|
foreach (@traject)
|
||||||
{
|
{
|
||||||
my @arg = split(" ");
|
my @arg = split(" ");
|
||||||
@ -974,7 +974,7 @@
|
|||||||
printf(PDB "%-11.11s", "P 1");
|
printf(PDB "%-11.11s", "P 1");
|
||||||
printf(PDB "%3.3s\n", "1");
|
printf(PDB "%3.3s\n", "1");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_atoms
|
sub pdb_atoms
|
||||||
{
|
{
|
||||||
@ -998,15 +998,15 @@
|
|||||||
foreach (@p) { $_ = 0 if (abs($_)<1e-4); }
|
foreach (@p) { $_ = 0 if (abs($_)<1e-4); }
|
||||||
printf(PDB "ATOM "); # pdb command
|
printf(PDB "ATOM "); # pdb command
|
||||||
printf(PDB "%6.6s ", ++$n); # atom number
|
printf(PDB "%6.6s ", ++$n); # atom number
|
||||||
printf(PDB "%-3.3s ",
|
printf(PDB "%-3.3s ",
|
||||||
$psf_ctrl ? $psf[4] : $names[$p[4]]); # atom name
|
$psf_ctrl ? $psf[4] : $names[$p[4]]); # atom name
|
||||||
printf(PDB "%-3.3s ",
|
printf(PDB "%-3.3s ",
|
||||||
$psf_ctrl ? $psf[3] : $residue[$nres]); # residue name
|
$psf_ctrl ? $psf[3] : $residue[$nres]); # residue name
|
||||||
printf(PDB "%5.5s ", $nres); # residue number
|
printf(PDB "%5.5s ", $nres); # residue number
|
||||||
printf(PDB "%3.3s ", ""); # empty placeholder
|
printf(PDB "%3.3s ", ""); # empty placeholder
|
||||||
printf(PDB "%7.7s %7.7s %7.7s ",
|
printf(PDB "%7.7s %7.7s %7.7s ",
|
||||||
$p[0], $p[1], $p[2]); # positions
|
$p[0], $p[1], $p[2]); # positions
|
||||||
printf(PDB "%5.5s %5.5s %4.4s ",
|
printf(PDB "%5.5s %5.5s %4.4s ",
|
||||||
"1.00", "0.00", ""); # trailing variables
|
"1.00", "0.00", ""); # trailing variables
|
||||||
printf(PDB "%-4.4s\n",
|
printf(PDB "%-4.4s\n",
|
||||||
$psf_ctrl ? $psf[1] : $cluster[$nres]); # cluster name
|
$psf_ctrl ? $psf[1] : $cluster[$nres]); # cluster name
|
||||||
@ -1015,7 +1015,7 @@
|
|||||||
};
|
};
|
||||||
printf(PDB "END\n");
|
printf(PDB "END\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub pdb_timestep
|
sub pdb_timestep
|
||||||
{
|
{
|
||||||
@ -1045,7 +1045,7 @@
|
|||||||
my $l = 0;
|
my $l = 0;
|
||||||
my $k = 0;
|
my $k = 0;
|
||||||
my @extra;
|
my @extra;
|
||||||
|
|
||||||
for (my $i=0; $i<$n; ++$i)
|
for (my $i=0; $i<$n; ++$i)
|
||||||
{
|
{
|
||||||
my @arg = split(" ", <DATA>);
|
my @arg = split(" ", <DATA>);
|
||||||
@ -1073,13 +1073,13 @@
|
|||||||
}
|
}
|
||||||
printf(PSF "\n");
|
printf(PSF "\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
sub psf_bonds
|
sub psf_bonds
|
||||||
{
|
{
|
||||||
my $npairs = 0;
|
my $npairs = 0;
|
||||||
|
|
||||||
delete_exclude() if (scalar(%exclude)>0);
|
delete_exclude() if (scalar(%exclude)>0);
|
||||||
delete_crossovers() if ($cut);
|
delete_crossovers() if ($cut);
|
||||||
printf(PSF "%8.8s !NBOND\n", scalar(@bonds));
|
printf(PSF "%8.8s !NBOND\n", scalar(@bonds));
|
||||||
foreach (@bonds)
|
foreach (@bonds)
|
||||||
@ -1098,7 +1098,7 @@
|
|||||||
initialize();
|
initialize();
|
||||||
|
|
||||||
# create .pdb file
|
# create .pdb file
|
||||||
|
|
||||||
$ncurrent = -1;
|
$ncurrent = -1;
|
||||||
while ($traject_flag&&!eof(TRAJECT))
|
while ($traject_flag&&!eof(TRAJECT))
|
||||||
{
|
{
|
||||||
@ -1134,4 +1134,4 @@
|
|||||||
|
|
||||||
close(TRAJECT);
|
close(TRAJECT);
|
||||||
close(DATA);
|
close(DATA);
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user