[gmx-users] GMXLIB does not induce residuetype.dat

[Ebert Maximilian]

Hi,
sorry for responding that late. The problem in the end was that first in specbonds the search length was 0.1nm off so it appeared for this structure as if the file wasn’t used but it was. and second i had the merge the PDB chain since there was a TER between the hetero atom and the protein residues.

so now all is good. putting in ~/.bash_profile 

GMXLIB=<path>

works fine. Thanks for your help,

Max

> On Oct 3, 2015, at 1:03 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> 
> The definition seems fine. In the pdb2gmx standard output, you should check
> that directory is the one being opened.
> 
> If it is, please do a "ls ${GMXLIB}" and check the output, if the file is
> there (and not inside the ff directory). Even though I am guessing this is
> just a typo problem, and you are using "residuestype.dat" while the file is
> "residuetypes.dat".
> 
> João
> 
> On Sat, Oct 3, 2015 at 4:55 AM, Barnett, James W <jbarnet4 at tulane.edu>
> wrote:
> 
>> On Thu, 2015-10-01 at 20:21 +0000, Ebert Maximilian wrote:
>>> Dear list,
>>> 
>>> I have my own force field working folder so I cloned the entire top
>> folder to
>>> no mess with the original files. I added residues to the residue type
>> file to
>>> add my residues to the protein group. My FF is included due to the GMXLIB
>>> environmental variable but my modified residuestype.dat not. Any idea
>> why?
>> 
>> Can you give an example of how it is not included? Is there a specific
>> GROMACS
>> command that is not finding it, or is it something else?
>> 
>> --
>> James “Wes” Barnett, Ph.D. Candidate
>> Louisiana Board of Regents Fellow
>> 
>> Chemical and Biomolecular Engineering
>> Tulane University
>> 341-B Lindy Boggs Center for Energy and Biotechnology
>> 6823 St. Charles Ave
>> New Orleans, Louisiana 70118-5674
>> jbarnet4 at tulane.edu
>> --
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> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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