[gmx-users] Re: gmx-users Digest, Vol 102, Issue 6

Jernej Zidar jernej.zidar at gmail.com
Wed Oct 3 07:15:46 CEST 2012

  Thanks for the tip. I turned the problem was caused by the PDB file.
It seems the water segment was not written properly (starting with
residue 1 and then all the way to the last one). After correcting this
and then manually editing the new PDB file to change the atom names
from TIP3 to SPCE water (i.e. OH2 -> OW ...), I was able to import the
PDB to Gromacs. I also passed the option "-renum" to pdb2gmx so the
atom numbering was corrected.

  Thanks for the tips!


On Tue, Oct 2, 2012 at 3:54 PM,  <gmx-users-request at gromacs.org> wrote:
> From: "Peter C. Lai" <pcl at uab.edu>
> Subject: Re: [gmx-users] pdb2gmx with more than 9999 residues
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20121002062613.GF94109 at cesium.hyperfine.info>
> Content-Type: text/plain; charset="us-ascii"
> A pdb file with a resid > 9999 exceeds the proper PDB format.
> You can resolvate a dry lipid bilayer using genbox fine; I don't know what
> problem you have with the solvation and minimization using that method,
> http://manual.gromacs.org/current/online/genbox.html
> You can also pdb2gmx or editconf the lipids and water separately as you
> suggested, then merge the files and run ediconf on the merged file to
> renumber the atoms.

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