[gmx-users] Docking Energy confirmation
baaden at smplinux.de
Thu Dec 4 09:06:01 CET 2003
this is very funny, because I am currently doing something very
similar/asking a similar question. I haven't tried it with Gromacs,
but as has been suggested by Ilya, you could use some implicit
solvent model (eg a simple sigmoidal dielectric via a user table)
to do so, or wait for Gromacs 4 with GB.
Another options (that I actually adopted) is to check autodock
results with STC (structural thermodynamics calculations) which
is available from U Pence. They also have a script (atd2stc I think
it is called) to cross-check autodock versus STC energies.
In that case the structure is not relaxed however but considered
NB: I don't have the STC website at hand, but with keywords STC and
Pence you should find it via google.
>>> Filipe Maia said:
>> I'm doing docking "calculations" with Autodock3.05.
>> My question is, is there any way to use the energy minimization procedure
>> Gromacs to relax the conformations obtained from autodock and have a
>> better estimate
>> of their energy (in comparision tothe energy that autodock gives as
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Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.marc-baaden.de
FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
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