Re: About Amber force fields

From: Jan Saam (
Date: Sat Jan 19 2008 - 23:00:45 CST


the intercompatibility of force fields is independent of the simulation
program. All that matters is if the program supports the data format of
the files and if it supports the functional forms of the equations
required by the force field. If one force field was designed to work
with another and you can read in all files, it should work.

In your case, if all input files are in AMBER format you should be fine
since NAMD can read those files. But I have too little experience with
GAFF and FF99SB to tell you if they work together well, but my
understanding is that they are made to be compatible.


Francesco Pietra wrote:
> As I am carrying out MD of protein complexes embedded in POPC and other
> membranes built with VMD, I would like to make use of NAMD. My question is:
> While Paratool pluging is being adapted to general use thanks to Jan Saam,
> which is the present status of NAMD with respect to carrying out MD with Amber
> force fields (which I am currently using)? Specifically, I make use of ff99SB
> for the protein, while the non-polymeric organic ligands are based on GAFF ff
> (Antechamber). I.e., I am stuck at a single residue for the ligand, which is
> not the best in case of large ligands as in my studies. Does the
> inter-compatibility ff99SB/GAFF hold for NAMD as well? At any event, I would
> consider that latter as a transition before Paratool.
> I really posed a more restricted question on the same subject long ago. Now I
> have acquired experience with MD on such systems, which means that I may be
> better prepared to the shift.
> Thanks
> francesco pietra
> ____________________________________________________________________________________
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Jan Saam
Theoretical and Computational Biophysics Group 
3061 Beckman Institute
University of Illinois
405 N. Mathews Ave
Urbana, IL 61801
Phone: (217) 244-1928
Fax:   (217) 244-6078

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