Hi,
I might be misinterpreting your question -- I'm assuming you want to
convert a system from Amber to run in CHARMM. If you have a
coordinate file which CHARMM understands (pdb or charmm format), and
you're using a standard biopolymer which you know the sequence of,
then you don't necessarily need a topology/psf file for CHARMM to
work, if you write a CHARMM input file correctly.
Unlike Amber where sander requires a prmtop file made by leap, CHARMM
has leap-esque topology
generating facilities built into the main program. You probably need
to read the charmm docs to figure this out.
Apologies if you're an experienced CHARMM user and I've got the wrong
end of the stick,
Dave
---- Message from HL Eastwood <s0237717.sms.ed.ac.uk> at 2005-02-16
17:19:56 ------
>Dear amber users
>
>I have an amber derived pdb file and corresponding amber paramater
file. Is it
>possible for me to generate a charmm parameter file from this data?
>
>An entry in the amber archive posted by Roass Walker suggests using
ptraj:
>
>"...you would want the following input file for ptraj (for amber to
charmm):
>
>trajin inputtrajectory.traj.gz
>trajout outputtrajectory charmm "
>
>I have done this and it generates a binary trajectory file for
charmm. However,
>I still require the paramater file. Any suggestions on how to get
this?
>
>thanks
>
>Hayden Eastwood
>Perdita Barran Reasearch Group
>Edinburgh University
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Received on Wed Feb 16 2005 - 18:53:01 PST
