Dear all,
I've been starting testing steered MD for some systems in order to apply
it for protein-protein interactions analysis and I've been searching the
literature on this topic. I have some related questions, which maybe you
could help me to answer.
1. Force of pulling proteins or receptor/ligand apart. In AMBER 10
manual example the constant of 5000 kcal/(mol A^2) is used. In the
literature I've seen absolutely different ranges of these values (down
to 1kcal/(mol A^2)). The explanations are a bit controversial: in some
papers the authors claim that the constant should be comparable to kT/2,
in other that this constant should be essentially higher in order to
have less effects from thermal motions. What do you think is appropriate
and what is the best way to optimize this constant for each individual
system? For pulling ion apart from the protein I noticed quite a
significant influence of this constant on the calculated free energy.
2. Speed of pulling. Again, I found various values in the literature
with the range from 1 to 100 A/ns. Am I right if I consider an ability
of the simulation to keep the structures of pulled apart proteins
undistorted as one of the most important criteria for the selection of
this parameter?
3. Is there an explicit way in AMBER (I use AMBER 10) to apply the
pulling forces to the centers of masses of protein/protein pair or to
all backbone atoms instead of choosing only two atoms? Otherwise could
an alternative solution be just putting restraints on backbone or
C-alpha atoms of the proteins and applying the pulling force on two
atoms (though this sounds to me being physically more ambiguous)?
4. Is there the way in Leap to create an assymetric water box for PBC
with an elongated side, along which the pulling is occuring? This would
save the computational expenses a lot in case of SMD.
Thank you very much in advance!
Best regards,
Sergey
--
Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax: (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Tue Jul 26 2011 - 03:00:02 PDT
