Subject: Re: CCL:Using Amber ff in NAMD

From: "Peter Gannett" <pgannett{at}hsc.wvu.edu>
Date: Wed, 02 Jun 2004 16:50:27 -0400

Jeny:

Yes, I've used it.  I haven't used Charmm but have used amber a long
time.  Amber splits a molecule into a coordinate file and a topology
file (I thought most programs like charmm, sybyl, insight...) also did
this, but maybe I'm mistaken.  You will have to construct these files. 
Perhaps babel will take your charmm files and write out amber files
(babel will do this but i don't know how good a job it does). 
Alternatively, you can get moil-view (
http://morita.chem.sunysb.edu/~carlos/moil-view.html ) which can read
pdb/charmm/amber files and can write amber coordinate and topology
files.

Which force field to use is a tough question to answer.  I do DNA and
use parm99.  Perhaps consult the literature and see what people seem to
be using for this type of problem.

Pete Gannett

>>> <jz7{at}duke.edu> 6/2/2004 1:28:03 PM >>>
Dear all,

Has anyone used Amber force field in NAMD calculation? I feel a little
bit
confused: When using Charmm in NAMD, we have topology file to build
structure (generate psf file), and parameter file to do calculation.
But
when goes to Amber, what is the corresponding topology file? And how
about
the format of the tcl or inp file to generate psf file? Which of the
parameter files is the best for protein-DNA system? (like parm99.dat,
parm99EP.dat, etc.)

Thanks a lot for your kind help!

Best,
Jeny

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