[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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