[gmx-users] improper dihedral angle in charmm and opls aa
Tom
dnaafm at gmail.com
Fri Feb 10 23:54:00 CET 2012
Dear Gromacs Users
I am confused about definition of improper dihedral angle in charmm27,
which is compared to oplsaa.
Why charmm ff in gromacs give *double* items for the same dihedral angle.
e.g. for charmm27 ASN
CG ND2 CB OD1
CG CB ND2 OD1
ND2 CG HD21 HD22
ND2 CG HD22 HD21
in opls aa for ASN
CG CB CA C dih_ASN_chi1_C_C_C_CO
CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
Thanks for advance!
Tom
PS:
the detail is as follows
------------------------------------------------
*in charmm27.ff/aminoacids.rtp*
[ ASN ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CC 0.55 7
OD1 O -0.55 8
ND2 NH2 -0.62 9
HD21 H 0.32 10
HD22 H 0.30 11
C C 0.51 12
O O -0.51 13
[ bonds ]
CB CA
CG CB
ND2 CG
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
ND2 HD21
ND2 HD22
C O
CG OD1
[ impropers ]
N -C CA HN
C CA +N O
CG ND2 CB OD1
CG CB ND2 OD1
ND2 CG HD21 HD22
ND2 CG HD22 HD21
[ cmap ]
-C N CA C +N
-------------------------------------------
in* oplsaa.ff/aminoacids.rtp*
[ ASN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_235 0.500 3
OD1 opls_236 -0.500 3
ND2 opls_237 -0.760 4
HD21 opls_240 0.380 4
HD22 opls_240 0.380 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ASN_chi1_N_C_C_C
CG CB CA C dih_ASN_chi1_C_C_C_CO
CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
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