AMBER Archive (2009)

Subject: Re: [AMBER] AMBER FF and NAMD

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Fri Oct 16 2009 - 09:45:25 CDT

On Fri, 2009-10-16 at 16:26 +0200, stefano_elli_at_libero.it wrote:
> 1) I have no a gaussian licence, I'll try to calculate RESP charges with gamess.
> My first question is possible to do so?

Yes.

> 2) I'm trying to use gaff force field to have some reference structure.
> I understand that GAFF doesnt' use wdv 10-12 to describe h-bond, but when I start
> the MD simulation NAMD (2.6 version) read xxx number of h-bond.
> Surprisingly the job work,...because I read on the NAMD manual that
> its doesn't like this kind of potential...

Wasn't that actually just a warning similar to the following?

Warning: Encounter 10-12 H-bond term
Warning: Found xxxxx H-H bonds.

If you have created the topology file with leap the 10-12 parameters
should be zero. Possible that NAMD tries to read the corresponding
flags but it doesn't have support for 10-12 parameters anyway.

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