[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

[Justin A. Lemkul]

francesca vitalini wrote:
> 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.

The topology format is largely unaffected by differences in version.  A few 
moments with a text editor to fix the #include statements written by a version 
in the 4.5.x series would solve any problems.

> 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?

Check the .rtp file - your atom is named in a way that is inconsistent with what 
the force field expects.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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