[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

[Justin A. Lemkul]

francesca vitalini wrote:
> 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?
> 

You still have to fix the incorrect atom name(s), regardless of version.  You 
can use a new version to make use of pdb2gmx -ter, if necessary.  Otherwise, 
your version should work for what you need.

-Justin

> 
> 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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> 
> 
> 

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

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

========================================