Re: Protein-ligand simulation

From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Jul 06 2013 - 13:28:15 CDT

Really nicely laid out, definitely a great resource!

On Sat, Jul 6, 2013 at 12:49 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:

> Thanks Chris,
>
> This tutorial will be useful for many other users
>
> Branko
>
>
> On 7/6/2013 10:02 AM, Chris Chipot wrote:
>
> James, Yeping, Flavio,
>
> check out the announcement on http://www.ks.uiuc.edu/ (and the link).
>
> Enjoy,
>
> Chris Chipot
>
>
>
> On 6/24/13 8:15 PM, James Starlight wrote:
>
> Chris, thanks you! I'll be very thankful for your tutorial!
>
> By the way what is the current most useful way to obtain charm parameters
> for small ligand-like compounds (starting from its full atomic pdbs with
> hydrogens) ?
> With Gromacs (using charm36 force field) typically I use swiss-param
> server which also produce PRM files in addition to the gromacs topology.
>
>
> James
>
> 2013/6/24 Chris Chipot <chipot_at_ks.uiuc.edu>
>
>> James,
>>
>> a NAMD tutorial for protein-ligand standard binding constant calculations
>> is currently in alpha-version. It will be tested thoroughly in the coming
>> days.
>>
>> If you can wait a little, I should be able to send you a copy by the end
>> of
>> this week.
>>
>> Chris Chipot
>>
>>
>>
>> On 6/24/13 8:51 AM, James Starlight wrote:
>>
>>> Dear Namd users!
>>>
>>>
>>> I'd like to perform simulation of the protein-ligand complex ( In that
>>> case I'll deal with the water-soluble diffusional ligand). Could you
>>> provide me with some tutorial for such simulation ? ( in particular I'm
>>> looking for additional parameters which i should specify in the conf files).
>>>
>>>
>>> Thanks for help,
>>>
>>>
>>> James
>>>
>>
>>
>> --
>> _______________________________________________________________________
>>
>> Chris Chipot, Ph.D.
>> Theoretical and Computational Biophysics Group
>> Beckman Institute
>> University of Illinois at Urbana-Champaign
>> 405 North Mathews Phone: (217) 244-5711
>> Urbana, Illinois 61801 Fax: (217) 244-6078
>>
>> E-mail: chipot_at_ks.uiuc.edu
>> Christophe.Chipot_at_edam.uhp-nancy.fr
>> Web: http://www.ks.uiuc.edu/~chipot
>> http://www.edam.uhp-nancy.fr
>>
>> It is hard for France to maintain a thirty-five-hour workweek when
>> China and India have invented a thirty-five-hour workday.
>> Thomas L. Friedman
>> _______________________________________________________________________
>>
>>
>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 North Mathews Phone: (217) 244-5711
> Urbana, Illinois 61801 Fax: (217) 244-6078
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_edam.uhp-nancy.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.edam.uhp-nancy.fr
>
> It is hard for France to maintain a thirty-five-hour workweek when
> China and India have invented a thirty-five-hour workday.
> Thomas L. Friedman
> _______________________________________________________________________
>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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