[gmx-users] Re: gmx-users Digest, Vol 60, Issue 14

Alan alanwilter at gmail.com
Thu Apr 2 15:17:45 CEST 2009

Sorry, but that I sort of knew already dear Berk.
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
#ifdef _FF_CHARMM

and spce.itp NOT!

So, imagine someone running a MD with charmm and spce water and one will
have problems I guess.


On Thu, Apr 2, 2009 at 13:48, <gmx-users-request at gromacs.org> wrote:

> Hi,
> CHARMM will be included and fully supported in Gromacs 4.1.
> AMBER on the other hand is provided as an external package.
> This is mainly because is requires some residue renaming and other stuff
> that pdb2gmx does currently does not support.
> We want to support it, but we anyhow want to completely rewrite pdb2gmx,
> so this might take some time.
> Since AMBER is not included in the Gromacs package, the water itp files
> have no AMBER specific stuff them.
> Currently the proper way to use water models with AMBER in Gromacs is
> to replace the include in the top file; e.g. for e.g. tip3p:
> #include "tip3p.itp"
> by
> #include "ffamber_tip3p.itp"
> Sorry for the inconvenience,
> Berk
> Date: Thu, 2 Apr 2009 11:04:56 +0100
> From: alanwilter at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Water models for amber03
> 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?
> Cheers,
> Alan
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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