[gmx-users] trjconv problem

[Berk Hess]

Hi,

It is not a pdb2gmx feature, but a global one.
pdb2gmx is only affected in the sense that it retains the residue numbers from the input pdb.
I assume those will be different for most lipid pdb files (if you use pdb2gmx for those).
This renumbering is done by any program that needs to output or select global residue numbers.
Currently this is switchable with the env.var. I mentioned.
If you put this env.var. in your GMXRC, you can get things how you want them.
Adding an option to all programs is not a good idea.

But I am open for any suggestions on this issue.

There is something I don't get though.
In the problematic output the lipids can not be one single residue, but should be two or more residues.

Berk

> Date: Mon, 18 Jan 2010 10:31:19 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] trjconv problem
> 
> 
> 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).
> 
> -Justin
> 
> 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
> > 
> > 
> > ------------------------------------------------------------------------
> > New Windows 7: Find the right PC for you. Learn more. 
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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
> 
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