[gmx-users] Docking Energy confirmation

Marc Baaden baaden at smplinux.de
Thu Dec 4 09:06:01 CET 2003

Hi Filipe,

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
as is.

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 
 >> from
 >> Gromacs to relax the conformations obtained from autodock and have a 
 >> better estimate
 >> of their energy (in comparision tothe energy that autodock gives as 
 >> result)?
 >> -- 
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 >> The world owes younothing.  It was here first.
 >>           -- Mark Twain
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Marc Baaden

 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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