From: Wei Chen (cwbluesky_at_gmail.com)
Date: Fri Sep 10 2010 - 12:48:15 CDT
Using Leap in Amber, you can get a topology file (*.prmtop) and a
coordinate file (*.prmcrd). That is all you need. Then in the conf
file for namd:
amber on # Specify this is AMBER force field
parmfile *.prmtop # Input PARM file
ambercoor *.prmcrd #input coordinate file
You can find detail description in the namd manual.
On Fri, Sep 10, 2010 at 7:48 AM, Patargias, George <patargias_at_usf.edu> wrote:
> I am sorry if I repeat an already posted question.
> Do I understand correctly that in order to use the
> Amber FF parameters in NAMD, we need a
> parm*.dat file and an amber coordinate file?
> Do these files need to be in a special format?
> Dont we need to provide NAMD with a topology too
> (in the "structure" entry of the conf file).
> Thanks a lot.
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