[gmx-users] coordinate error

Berk Hess gmx3 at hotmail.com
Mon Sep 6 17:33:41 CEST 2004

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>CC: gmx-users at gromacs.org
>Subject: Re: [gmx-users] coordinate error
>Date: Mon, 6 Sep 2004 17:17:52 +0200 (CEST)
>You are (pdb2gmx is) mixing protein_a and protein_A. I'm not certain that
>will work. Try renaming some of your chains (half of them), if they are
>indeed different. Are they? Otherwise you may need to rearrange the
>molecules, such that you have fewer itp files. If your system consists of
>only 4 different protein molecultetypes you can also write
>and so on.

grompp is mixing the names.
grompp currently does not check on double molecule definitions.
This check should be implemented.

Another thing is if we want to keep grompp case insensitive
or if we want to make it case sensitive.
If we keep it case insensitive pdb2gmx should be modified
to write multiple-letter chains after ???_z.


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