AMBER Archive (2009)

Subject: Re: [AMBER] chain restrain x TI

From: Josmar R. da Rocha (
Date: Sat May 02 2009 - 12:09:53 CDT

Dear David,

Thanks for answering. I'm not quite sure. My guess is that since the enzime seems to be very flexible, may be when using only one monomer the movements can not be conpensate by the opposite movements from the other monomers, making that simulated monomer to relax too much.  Anyway, following your sugestion, since freezing the orher monomers would not speed up the simulation it's better to run the MD using the whole system. Thank you very much!

Josmar Rocha

--- Em qui, 30/4/09, David A. Case <> escreveu:
Does it make sense to only include the monomer with the ligand? An
alternative would be to use restraints on the other three monomers (say with
a restraint weight of something like 1.0 kcal/mol-A^2). Of course, that
doesn't speed up the calculation, but neither does using a belly. In
if you don't actually get rid of some parts of the system, you essentially
have to pay for simulating all of it.

..hope this helps...dac

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