[gmx-users] Preparation protein-ligand complex

[Thomas Evangelidis]

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html



On 1 March 2013 12:03, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Gromacs Users!
>
>
> During preparation of the protein-ligand complex (manual placement of
> the ligand into the ligand-binding pocket (based onto known x-ray
> data) I've forced with the overlap of some polar sidechains of the
> ligand interiour with big aromatic group of the ligand itself. I've
> tried resolve such clashes via energy minimization (both in the steep
> and cg algorithms) but spatial overlap has not been removed. Could you
> provide me with some possible ways to remove such clushes manualy?
>
>
>
> James
> --
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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/