VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Sep 28 2015 - 21:26:00 CDT

Eddie,

TopoTools can duplicate a molecule an arbitrary number of times. Also, I believe that you can loop over the psfread <psf file> command using PSFGen.

Regards,
Christopher Mayne

On Sep 28, 2015, at 6:57 PM, Prof. Eddie 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.siue.edu_-257Eeackad&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=46F11OQdvQOAMiHHYn-HroU_vVQClNfsF_2XrYxN46c&s=EmoIpqW0tt9dmbqq8Q0IE2T_ug42bg_p9LeMN5zyxjw&e=>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390