Dear Ross,
Thanks a lot. Indeed I am aware of the 1-4 differences (NAMD for example is
clear about it when using amber ff). Usually, when users ask me this
question I always suggest trying to run systems with all amber compatible ff
(e.g. amber99sb + gaff) and then compare with results of mix charmm + gaff.
This would be a result there I would love see publish.
Thanks again, all the best,
Alan
On 8 September 2010 19:03, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Alan,
>
> In principal there is no reason why one can't mix these two force fields.
> The equations are suitably similar that it should work, however how well
> the
> actual charge models interact is probably open to lots of debate.
>
> One key requirement is that the scaling of 1-4 interactions is different in
> GAFF to in CHARMM. For GAFF 1-4 EEL is divided by 1.2 and 1-4 VDW by 2.0.
> CHARMM does not employ any scaling but instead uses different parameters
> for
> 1-4 VDW interactions. In principal these two force fields can be mixed
> 'correctly' in AMBER 11. One would probably have to hack the prmtop a bit
> to
> get it to work properly but there is now support for the 1-4 scaling to be
> different for each dihedral type. I have not tried this mixing myself
> though
> and one should consider it an advanced topic.
>
> So I think the real question is not so much if one can correctly mix these
> two force fields but whether the interaction between something described
> with CHARMM and something described with GAFF is correct. I.e. H bonding
> between a GAFF ligand and a CHARMM protein for example.
>
> This is really just something that would have to be carefully tested but I
> see no reason why it would not work okay.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Alan [mailto:alanwilter.gmail.com]
> > Sent: Wednesday, September 08, 2010 10:36 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] mixing GAFF with CHARMM
> >
> > Hi there,
> >
> > As the developer of ACPYPE (a tool for adapting antechamber topologies
> > generated to other MD engines) I usually see people asking me about
> > mixing
> > GAFF with CHARMM.
> >
> > I myself do some sort of mixing buy using GAFF with CNS (Engh & Huber
> > parameters) but I believe I know what I am doing. However, I never used
> > Charmm so...
> >
> > Well, what I am looking is for advices and maybe references concerning
> > this
> > topic. How tabu is this and what would be the implications and
> > potential
> > problems. For example, AFAIK oplsaa and amber/gaff have a lot in common
> > (ok
> > parameters -- bonded and nonbonded -- may differ, but sometimes just
> > slightly, however topology -- in the sense how atoms are connected --
> > is
> > very similar if not the same!).
> >
> > Many thanks in advance,
> >
> > 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.
> > >>http://www.bio.cam.ac.uk/~awd28<<
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed Sep 08 2010 - 14:30:12 PDT
