On Mon, May 5, 2014 at 4:44 AM, sammia khatak <saammia_kt.hotmail.com>wrote:
> Hello
> I am running energy minimization of protein ligand complex. Is there a way
> to generate psf file from pdb file which is actually a protein ligand
> complex in water box and if it is so then how? secondly either way if i
> just generate psf file of protein ligand complex separately and waterbox
> separately. will it work?
> suggest eitherway.
>
Why do you want to create a PSF file? NAMD reads Amber topology files if
you need to use NAMD to run your calculations (see the webpage that Dave
sent you in your last email). I don't know of any tool that lets you
define a PSF file for use with the Amber force field, and minimizing with
the Amber force field before running MD with the CHARMM force field is a
bad idea -- you should be consistent in your force field use for every step.
In any case, if you want to pursue what you asked about specifically (i.e.,
creating a PSF file for use with NAMD or CHARMM), this is not the best
forum to ask. Amber contains no tools to do what you want and few people
here have experience with PSF creation and PSF compatibility between
different programs.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 05 2014 - 03:30:03 PDT
