VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Sep 29 2015 - 10:42:58 CDT

Thanks Christopher,
I was hoping there was a way of using the existing machinery in vmd before
writing a custom tcl script which I believe will have to load the
coordinates with the pdb displace the ligand and repeat.
If you know of something already written for this purpose please let me
know.
Thanks,
Eddie

On Mon, Sep 28, 2015 at 9:26 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> 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
>
>
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390