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bug fix for enumerating Urey-Bradley bonds

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This commit is contained in:
Steve Plimpton
2022-03-07 11:02:44 -07:00
parent 5c10b621b3
commit 7087dfc019
3 changed files with 2841 additions and 2840 deletions
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5670
examples/amoeba/data.ubiquitin
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7
examples/amoeba/in.ubiquitin
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@ -14,14 +14,15 @@ improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO # per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes fix amtype all property/atom i_amtype ghost yes
fix pitorsion all pitorsion #fix pitorsion all pitorsion
fix extra all property/atom & fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe fix extra2 all property/atom i_polaxe
read_data data.ubiquitin fix amtype NULL "Tinker Types" & read_data data.ubiquitin fix amtype NULL "Tinker Types"
fix pitorsion pitorsions PiTorsions #read_data data.ubiquitin fix amtype NULL "Tinker Types" &
# fix pitorsion pitorsions PiTorsions
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key

4
tools/tinker/tinker2lmp.py
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@ -782,10 +782,10 @@ for atom1,atom2,atom3 in ublist:
if (c1,c2,c3) in ubdict: if (c1,c2,c3) in ubdict:
m,params = ubdict[(c1,c2,c3)] m,params = ubdict[(c1,c2,c3)]
blist.append((c1,c3)) blist.append((atom1,atom3))
elif (c3,c2,c1) in ubdict: elif (c3,c2,c1) in ubdict:
m,params = ubdict[(c3,c2,c1)] m,params = ubdict[(c3,c2,c1)]
blist.append((c3,c1)) blist.append((atom3,atom1))
if not flags[m]: if not flags[m]:
v1,v2,v3,v4 = params[3:] v1,v2,v3,v4 = params[3:]