[gmx-users] RE: rather theoretical question

[Ing. Vojtěch Spiwok]

>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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