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

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 18 2008 - 12:09:48 CDT

On Fri, 18 Jul 2008, tinni sona wrote:

TS> Hi All,
TS>
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>
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.

cheers,
   axel.

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

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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