[gmx-users] getting a good .gro file from a pdb file while the topology is ready

[van Bemmelen]

Hi,

I've noticed this too and indeed it can be a bit irritating. For
example: editconf doesn't recognize the HOH residue when changing the
box density (see also
http://www.gromacs.org/pipermail/gmx-users/2007-January/025611.html).

Of course it's not a big problem, and maybe there's a very good reason
why pdb2gmx is doing this. Then again, if not, maybe it can be changed.

Thanks,
Jeroen


>Date: Wed, 3 Oct 2007 19:09:54 -0400
>From: Allen Smith <easmith at beatrice.rutgers.edu>
>Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>	while the	topology is ready
>To: gmx-users at gromacs.org
>Message-ID: <mid+200710032309.l93N9sL21343576 at dogberry.rutgers.edu>
>Content-Type: text/plain; charset=us-ascii
>
>[...]
>
>P.S. Incidentally, I note the irritating habit of pdb2gmx (including in
>3.3.2) of converting what is already labeled as SOL to HOH, 
>even though genbox inserts water molecules as SOL.
>
>-- 
>Allen Smith