[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

[francesca vitalini]

Hi all!
I'm trying to create a topology file from the pdb using the pdb2gmx
command of gromacs 3.3.1 but I'm encountering some issues. I should
use the flag -tar in order to select interactively the termini, but
with the old version of gromacs this is not implemented and I cannot
use a new one because I need the reverse transformation tool which is
only implemented in that version.
Here it is the pdb I'm using

REMARK
ATOM      1 1HH3 ACE     1      -3.547   1.520   1.054
ATOM      2  CH3 ACE     1      -3.081   0.536   0.999
ATOM      3 2HH3 ACE     1      -3.437   0.016   0.110
ATOM      4 3HH3 ACE     1      -3.348  -0.041   1.883
ATOM      5  C   ACE     1      -1.570   0.683   0.929
ATOM      6  O   ACE     1      -1.051   1.800   0.938
ATOM      7  N   ALA     2      -0.862  -0.446   0.851
ATOM      8  H   ALA     2      -1.368  -1.322   0.859
ATOM      9  CA  ALA     2       0.607  -0.509   0.828
ATOM     10  HA  ALA     2       0.997   0.272   1.484
ATOM     11  CB  ALA     2       1.025  -1.867   1.412
ATOM     12 1HB  ALA     2       2.113  -1.918   1.485
ATOM     13 2HB  ALA     2       0.676  -2.677   0.770
ATOM     14 3HB  ALA     2       0.604  -1.990   2.411
ATOM     15  C   ALA     2       1.238  -0.262  -0.565
ATOM     16  O   ALA     2       2.465  -0.181  -0.678
ATOM     17  N   NAC     3       0.423  -0.139  -1.620
ATOM     18  H   NAC     3      -0.569  -0.212  -1.447
ATOM     19  CH3 NAC     3       0.860   0.098  -2.992
ATOM     20 1HH3 NAC     3       1.413   1.037  -3.050
ATOM     21 2HH3 NAC     3       1.506  -0.718  -3.323
ATOM     22 3HH3 NAC     3      -0.006   0.155  -3.652
TER
END


And this is the pdb2gmx command
path/pdb2gmx -ignh -missing -f struct1-1.pdb -p ala.top -o ala.gro


I use the gromos9653a6 forcefield and the spc water model

And this is the error I get

There are 2 donors and 2 acceptors
There are 2 hydrogen bonds
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2gmx.c, line: 383

Fatal error:
Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms
             while sorting atoms
-------------------------------------------------------

Any suggestions?
Thanks



-- 
Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412