Sorry, but that I sort of knew already dear Berk.<div><br></div><div>The very particular thing that I observed is if you compare spc.itp and spce.itp from GMX 4.0.4, you will notice that spc.itp has<div><br></div><div><div>
#ifdef _FF_CHARMM</div><div>...</div><div><br></div><div>and spce.itp NOT!</div><div><br></div><div>So, imagine someone running a MD with charmm and spce water and one will have problems I guess.</div><div><br></div><div>
Alan</div><br><div class="gmail_quote">On Thu, Apr 2, 2009 at 13:48, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Hi,<br>
<br>
CHARMM will be included and fully supported in Gromacs 4.1.<br>
AMBER on the other hand is provided as an external package.<br>
This is mainly because is requires some residue renaming and other stuff<br>
that pdb2gmx does currently does not support.<br>
We want to support it, but we anyhow want to completely rewrite pdb2gmx,<br>
so this might take some time.<br>
<br>
Since AMBER is not included in the Gromacs package, the water itp files<br>
have no AMBER specific stuff them.<br>
<br>
Currently the proper way to use water models with AMBER in Gromacs is<br>
to replace the include in the top file; e.g. for e.g. tip3p:<br>
#include "tip3p.itp"<br>
by<br>
#include "ffamber_tip3p.itp"<br>
<br>
Sorry for the inconvenience,<br>
<br>
Berk<br>
<br>
Date: Thu, 2 Apr 2009 11:04:56 +0100<br>
From: <a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Water models for amber03<br>
<br>
I was reviewing *.itp from GMX 4.0.4 and found that we now have _FF_CHARMM in, e.g., tip3p.itp and spc.itp, but not in spce.itp, why not? Was it forgotten? Anyone would kindly know something about it?<br>
<br>
<br>
Cheers,<br>
Alan<br></blockquote></div>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div></div>