VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Sep 28 2015 - 20:56:21 CDT

Hi Eddie,

What I believe you could do is use the *.top file that FFTK creates for
you. You could use psfgen wherein you read the FFTK-generated top file
(along with standard CHARMM top files) and generate a fresh psf. Only thing
is, you need to make sure your top file is updated (i.e. has the charges
etc).

Regards,
Chitrak.

On Mon, Sep 28, 2015 at 7:57 PM, Prof. Eddie <eackad_at_siue.edu> wrote:

> Hi all,
> I used fftk to parameterize a ligand and now I want to make a box with a
> bunch of them. I realize I need to take the pdb and add displaced copies
> (change x/y/z and atom number accordingly), but what about the psf? Is
> there a "simple" way to take my fftk psf and make multiple copies (or at
> least tell the autopsf script how to find the parameters for one copy). If
> there isn't I can just do it the hard way, but I'd like to know I'm not
> trying to reinvent the wheel.
> Thanks,
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
>