[gmx-users] trjconv problem

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 18 16:31:19 CET 2010

Could renumbering be a switchable feature?  For instance, pdb2gmx -[no]renumber, 
with "no" being default?  Otherwise, could you provide an example of how to 
properly use the environment variable you posted, since this would seem to 
affect all of us in the membrane protein world quite distinctly (i.e., a 
singly-numbered lipid, as reported, kills many of the programs we have written 
for lipid analysis).


Berk Hess wrote:
> Hi,
> This is a feature.
> For a long time users have been complaining that pdb2gmx renumbers the 
> residues in a protein.
> I have now changed this such that the residue numbers in the pdb are 
> retained.
> But for for instance solvent you would not like to have this behavior.
> So I decided to keep numbering single-residue molecules.
> If you also want you lipids to continue numbering, you'll have to set 
> the env.var. GMX_MAXRESRENUM
> to the number of residues in a lipid.
> Berk
> ------------------------------------------------------------------------
> Date: Mon, 18 Jan 2010 13:05:42 -0200
> From: stefhoor at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] trjconv problem
> I am trying to use trjconv to extract frames from my protein/membrane 
> system in order to analyse with gdmat. Before using git's latest gromacs 
> version, everything worked just fine. But now, every coordinate file 
> trjconv gives me has the DPPC lipid molecules without numbering. It is 
> like if my membrane was formed of a single DPPC (huge) residue. So 
> instead of generating DPPC residue 1, 2, 3, 4 ....etc, trjconv gives me 
> DPPC residue 1 with 5000 atoms.
> Some light on the matter would be great.
> Thanks
> ------------------------------------------------------------------------
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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