Re: CCL:Using Amber ff in NAMD

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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