[gmx-users] doubt about the ffencadv.rtp

[Mark Abraham]

Serena Leone wrote:
> Dear all,
> 
> I was trying to model a peptide that I built from scratch with Chimera 
> to use in some simulation with Gromacs 4 (encad vacuum ff). After 
> moduifying the atom names in the pdb accordingly to rtp for 
> ffencadv.rtp, I keep obtaining this error from pdb2gmx:
> 
> Program pdb2gmx, VERSION 4.0
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom H not found in residue 3 while adding improper
> 
> Residue 3 in my case is a Pro, and, not being terminal, it is not 
> supposed to have an amide H. Now, I know that is usually not recommended 
> to play with the ff rtp files, but it seems to me an error in the rtp, 
> that maybe needs to be corrected:
> 
> rtp entry:
> 
> [ PRO ]
> [ atoms ]
>     N    N     0.000     0
>    CA    C1   -0.119     1
>    HA    H     0.119     1
>    CB    CP   -0.238     2
>   HB1    H     0.119     2
>   HB2    H     0.119     2
>    CG    CP   -0.238     3
>   HG1    H     0.119     3
>   HG2    H     0.119     3
>    CD    CP   -0.238     4
>   HD1    H     0.119     4
>   HD2    H     0.119     4
>     C    Aprime    0.380     5
>     O    O    -0.380     5
> [ bonds ]
>     N    CA
>    CA    HA
>    CA    CB
>    CA     C
>    CB   HB1
>    CB   HB2
>    CB    CG
>    CG   HG1
>    CG   HG2
>    CG    CD
>    CD   HD1
>    CD   HD2
>    CD     N
>     C     O
>    -C     N
> [ dihedrals ]
>   -CA     -C      N     CD
>   -C       N     CA      C
>    N      CA     CB     CG
>    N      CA      C     +N
>   CA      CB     CG     CD
>   CB      CG     CD      N
> [ impropers ]
>    -C     CA      N      H      improper_X_X_N_X
>     N      C     CA     HA      improper_X_X_C_X
>     N      C     CA     CB      improper_N_A_C1_C
>    CA     CG     CB    HB1      improper_X_X_C_X
>    CA     CG     CB    HB2      improper_X_X_C_X
>    CB     CD     CG    HG1      improper_X_X_C_X
>    CB     CD     CG    HG2      improper_X_X_C_X
>    CG      N     CD    HD1      improper_X_X_C_X
>    CG      N     CD    HD2      improper_X_X_C_X
>    -C     CD      N     CA      improper_X_X_N_X
>    CA     +N      C      O      improper_X_X_A_X
> 
> Now, my guess would be, to describethe same improper, that it should read:
> 
> -C     CA      N      CD      improper_X_X_N_X
> 
> instead of
> 
> -C     CA      N      H      improper_X_X_N_X
> 
> am I right, or am I overlooking something?

I don't know anything about this force field, but the line under 
discussion was not present in 3.3.x versions of GROMACS. Improper 
dihedrals are used to help enforce planarity of four atoms. As such, 
only two are required to keep -CA, -C, -O, N, H, CA moiety coplanar 
given the existence of a -CA, -C, N, C normal dihedral. All the other 
peptide linkages have only the two impropers as indicated in the last 
two lines of [impropers] for PRO above. Thus, I think this proline 
residue topology got broken in the source distribution between the 3.3.1 
  version I'm looking at, and 4.0.

Mark