Re: how to generate psf file using the AMBER topology file

From: Axel Kohlmeyer (
Date: Fri Jul 18 2008 - 12:09:48 CDT

On Fri, 18 Jul 2008, tinni sona wrote:

TS> Hi All,
TS> I want to perform the MD simulation of protein-carbohydrate complex using
TS> NAMD. My force field is AMBER. I'm failed to generate the required psf file
TS> for the system using the AMBER and GLYCAM topology files for protein and
TS> carbohydrate. However using CHARMM topology file for protein the psf file
TS> for protein is generating nicely.
TS> Can anyone please suggest me how to generate the psf file using topology
TS> file taken from AMBER?

why do that??

NAMD can read the AMBER generated topology file directly.
check out the documentation.


TS> I would really appreciate if you could respond.
TS> Thanks,
TS> Madhurima

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:04 CST