[gmx-users] RE: rather theoretical question

[Dmitry Egorov]

Dear Ing. Vojtěch Spiwok, thank you very much for your answer. It is useful
for me.
D. Egorov.
----- Original Message -----
From: Ing. Vojtěch Spiwok <Vojtech.Spiwok at vscht.cz>
To: <gmx-users at gromacs.org>
Sent: Thursday, July 03, 2003 4:43 PM
Subject: [gmx-users] RE: rather theoretical question


> >Dear Gromacs users, could anybody answer next question.
> >
> >Suppose, we have two different conformations of the same enzyme-cofactor
=
> >complex,say, C1 and C2. Further, conformations of ligand binding sites =
> >and ligands themselves are also different for these C1 and C2 states. =
> >Then we place,say, ligand in conformation from C2 to binding site of C1 =
> >( with previously deleted C1 ligand ). How is it reasonable  to wait =
> >that MD convert C2 ligand conformation to right for receptor C1 state =
> >and reproduce right ligand fit. What complications may occur here.
> >
> >Thanks for your attention to my problem.
> >D. Egorov
>
> It depends especialy on size of the ligand and the conformational change.
> If there are some sterical bumps between C1 ligand and C2 site you can
> experience high forces and thus high velocities and possible crashes of
the
> program. You must thoughtfuly minimise the complex, do some MDs with
> constraints and possibli try number of initial orientation of the ligand.
>
> Hope will help
> Vojtech Spiwok
> ???????? ??????????? ?????????? ?????
>
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