From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sat Jul 06 2013 - 03:02:05 CDT
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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