49 lines
2.1 KiB
Plaintext
49 lines
2.1 KiB
Plaintext
# The oplsaa2024.lt file contains force-field parameters, atom type definitions,
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# partial charges, masses and bond-angle rules for the atoms in your system.
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import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
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# It defines these atom types:
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# atom-type charge mass btype epsilon sigma description
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# @atom:235 0.5 12.011 C~ 0.105 3.75 "C: C=O in amide. Acyl R in amides"
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# @atom:236 -0.5 15.999 O~ 0.21 2.96 "O: C=O in amide. is neutral - use"
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# @atom:237 -0.76 14.007 N~ 0.17 3.25 "N: primary amide. alkane params"
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# @atom:240 0.38 1.008 H~ 0 0 "H on N: primary amide"
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# @atom:279 0 1.008 HC 0.03 2.42 "AA H-alpha in aldehyde & formamide"
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# (Note: Future versions of OPLSAA might use different @atom type numbers.)
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_FAM inherits OPLSAA {
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# atomID molID atomType charge coordX coordY coordZ
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write('Data Atoms') {
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$atom:C00 $mol @atom:235 0.00 0.100014490 0.490422099 0.0
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$atom:O01 $mol @atom:236 0.00 1.091153187 -0.250749643 0.0
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$atom:N02 $mol @atom:237 0.00 -1.121616690 -0.181085754 0.0
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$atom:H03 $mol @atom:240 0.00 -2.013715893 0.272535813 0.0
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$atom:H04 $mol @atom:240 0.00 -1.056768463 -1.190185868 0.0
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$atom:H05 $mol @atom:279 0.00 0.144676387 1.570292021 0.0
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}
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# Note: You don't have to specify the charge in this example because we are
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# using the OPLSAA force-field which assigns charge according to
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# atom-type. Just leave these numbers as 0.00 for now.
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# Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number).
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# If we put "$mol" there, moltemplate will generate this integer for you
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# A list of the bonds in the molecule:
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# BondID AtomID1 AtomID2
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write('Data Bond List') {
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$bond:C1 $atom:C00 $atom:O01
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$bond:C2 $atom:C00 $atom:H05
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$bond:C3 $atom:C00 $atom:N02
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$bond:C4 $atom:N02 $atom:H03
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$bond:C5 $atom:N02 $atom:H04
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}
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# In the "Data Bond List" section we don't have to specify the bond type.
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# Bond types will be determined by the atom type (according to oplsaa2024.lt).
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}
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