VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 05 2015 - 07:24:10 CDT
On Tue, May 5, 2015 at 7:48 AM, δΈζ <dingh09_at_163.com> wrote:
> I create the molecules in one pdb successfully. But I can't create the psf
> file for such a pdb file with autoPSF plugin. So what should I do to create
> a psf file?
this cannot be easily answered in full generality. suitable steps
depend on the force field that you plan to use and whether there are
suitable topology files for use with psfgen. autopsf is an automated
way to run psfgen, so you should first read the psfgen documentation
and tutorial(s) to see how it works and whether it is applicable to
your case. otherwise, you need to tell us what you need the psf file
for. in principle a psf file can be generated for almost any structure
with some scripting and knowledge of the force field. but in that
case, you will also need a suitable parameter file to be used with the
matching software that you want to use the .psf file with.
> Thank you!
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.