[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

[francesca vitalini]

Do you mean that I can just use the new version of pdb2gmx than change
the included forcefield and in case the name of the atoms and it
should work?


2012/2/16 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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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-- 
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