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 <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] getting a good .gro file from a pdb file > while the topology is ready >To: gmx-users@gromacs.org >Message-ID: <[EMAIL PROTECTED]> >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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
