VMD-L Mailing List
From: Tim Lo (timlo_at_connect.hku.hk)
Date: Fri Oct 02 2015 - 21:35:39 CDT
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Hi Eddie,
Please read
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2.
TopoTools is convenient to use. There are just few parameters you need
to change in the script in order to generate your desired box of molecules.
Cheers,
Tim
Research Associate
The University of Hong Kong
On 29/9/2015 23:42, Prof. Eddie wrote:
> 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 <mailto: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 <tel:%28618%29%20650-2390>
>
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
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