From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jun 24 2013 - 18:43:42 CDT
Clearly FFTK. :)
http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
On Jun 24, 2013, at 2:15 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
>
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> _______________________________________________________________________
>
>
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