[gmx-users] trjconv problem

Berk Hess gmx3 at hotmail.com
Mon Jan 18 16:17:07 CET 2010


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.


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.

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