From: Axel Kohlmeyer (
Date: Fri Jul 17 2009 - 07:23:35 CDT

On Fri, 2009-07-17 at 11:34 +0200, Yogesh Aher wrote:
> Dear Amber users,
> I searched the past archieves but couldn't find the relevant solution,
> so writing it again.
> I am facing bit complicated problem currently. We have some new MD
> software, but it is not accepting .prmtop and .prmcrd files as input
> for running the simulation.
> Instead, it says:
> "To allow your AMBER-simulated systems to be run, coordinates and
> structure files must be regenerated using VMD and the AMBER topology
> file in CHARMM format, as all input files must be in CHARMM format."
> Anyone has any idea how to deal with such case?

yep. check out the psfgen tutorials. all you'd need is the
corresponding AMBER parameter and topology files in CHARMM
format. they exist in several versions, so you may want to
check out the NAMD and VMD mailing archives or the web in
general for them.


> Thanking you,
> Sincerely,
> Yogesh

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.