[gmx-users] improper dihedral angle in charmm and opls aa

[Mark Abraham]

On 11/02/2012 9:54 AM, Tom wrote:
> 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

These are not duplicates. Atom ordering is significant. These *improper* 
dihedral angles are enforcing planarity of the amide moiety. This is 
done by influencing dihedral angles along intra-atom vectors where there 
is no bond. OPLS/AA is working differently somehow.

Mark

> 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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