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: [email protected]
To: [email protected]
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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