From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Sep 29 2015 - 10:39:22 CDT

Thanks Chitrak,
this allowed me to run the autopsf but it deletes all the other copies of
the ligand. I'll like to start with say 10 copies at different locations
and then use autopsf to generate the psf file for the system of 10.
Any ideas? Thanks again!
Eddie

On Mon, Sep 28, 2015 at 8:56 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> 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
>>
>
>

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