[gmx-users] Preparation protein-ligand complex

[James Starlight]

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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