[gmx-users] Interaction Energies for QSAR analisys

Monique Brito moniquebrito at yahoo.com.br
Fri Feb 10 18:34:02 CET 2006


We are doing MD simulations just for
obtaining the interaction energies
of a ligand-protein complex in vacuo.

The program that perform the ligand
topology, PRODRG available in web,
just works in the force field 
4 of the GROMACS (GROMOS 87), which
works with a water box.

Is there any problem in using this force
field for doing calculations in vacuo?
Is it necessary to add some parameter in 
.mdp file to correct the dielectric

We suppose that there is not any
problem, since the interaction energies
of a set of ligand-protein complexes
will be used in a QSAR analisys.

Thanks in advance,

  Msc. Monique Brito 
  Laboratório de Modelagem Molecular - LabMMol
  Instituto de Química - UFRJ
  Página profissional: http://modmol.cjb.net 
  Página pessoal: http://bancovazio.cjb.net


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