[gmx-users] Preparation protein-ligand complex

[Thomas Evangelidis]

You can add hydrogens after side-chain fixing with Chimera, but don't know
if it will preserve your atom names.
Why don't you start from the beginning, namely place the ligand in the
X-ray structure, fix clashing side-chains with Chimera, prepare the
topology with GMX tools and run EM?

T.

On 1 March 2013 15:21, James Starlight <jmsstarlight at gmail.com> wrote:

> Thomas,
>
> That Chimera's plugin always remove hydrogens from altered
> side-chains. Assuming that I'm using united atom force field with the
> specified atom names how I could preserve initial atom names as well
> as hydrogens after rotamer switching ?
>
>
> James
>
> 2013/3/1 Thomas Evangelidis <tevang3 at gmail.com>:
> >
> 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/
> > --
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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/