[gmx-users] doubt about the ffencadv.rtp

Serena Leone sleone at rics.bwh.harvard.edu
Mon Nov 3 21:46:36 CET 2008

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?

Thank you very much,

Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586

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