[gmx-users] Free energy profiles with Pull code : dimer/dimer interactions
CROUZY Serge 119222
serge.crouzy at cea.fr
Wed Nov 2 17:24:48 CET 2016
Dear gromacs users
In previous mail on the list Justin argued about free energy calculations with Pull code that:
"For general
protein-ligand complexes, it is *NOT* appropriate to assume
one-dimensional pulling or applying position restraints to the
protein. Our paper (from which the tutorial was derived) describes
the somewhat unique case we were dealing with. "
In my case, I'm calculating the profile for dimer dissociation in a
tetramer of proteins pulling on 1 dimer in direction X (because the
tetramer is oriented in a such a way that X is the principal axis)
while the other dimer is harmonically restrained (BB atoms only)
I don't see how this could be done differently; although I'm hoping that
the free energy will result from the sole force between dimer/dimer
atoms: the restraint on one dimer should not affect the result .. As
long as they do not prevent the fluctuations (breathing) necessary for an almost reversible extraction of
one dimer from the tetramer. Is there a paper describing the possible effect of
these restraints on the profile ? (I suppose if one dimer is
completely fixed, the energy barrier for extraction will increase
dramatically because its residues won't be allowed to adjust while the
partner dimer is pulled out)
Thanks for your input
Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble UMR CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K pièce 110
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT
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