From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat Jul 06 2013 - 11:49:45 CDT
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 <mailto: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
>> <mailto:chipot_at_ks.uiuc.edu>
>> Christophe.Chipot_at_edam.uhp-nancy.fr
>> <mailto:Christophe.Chipot_at_edam.uhp-nancy.fr>
>> Web: http://www.ks.uiuc.edu/~chipot
>> <http://www.ks.uiuc.edu/%7Echipot>
>> 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
> _______________________________________________________________________
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