AMBER Archive (2009)

Subject: [AMBER] AMBER FF and NAMD

From: stefano_elli\_at_libero\.it
Date: Fri Oct 16 2009 - 09:26:14 CDT


My name is stefano.

I'm trying to do some MD simulation of heparine like oligosaccharide in explicit water solution.
I'm using amber force fields with NAMD MD engine.

Ok the right force field to use is GLYCAM but...
The problem is that heparine like molecule are FULL of charges sulphated group,...and even glycam,...

1) I have no a gaussian licence, I'll try to calculate RESP charges with gamess.
My first question is possible to do so?

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...

So my question is

->There's a way to describe h-bond with gaff and NAMD?

Thank you for the answer


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