Dear AMBERs,
I have the following question: I'd like to study the conformational
behaviour of a part of a system, in particular, several terminal
residues of the protein, which are especially flexible. My idea is to
restraint the rest of the system after a minimization and to let the
terminus of interest to move in a REMD simulation in implicit solvent.
What would be the most efficient and most appropriate way to apply
restraints for the rest of the system? I checked already that it works
with ntr=1 and restraintmask applied to the part of the system I don't
want to let move, but it is pretty slow, and I wonder if there is a
better way to carry out such calculations. As far as I understand,
ibelly=1 cannot be used together with ntt=3 but neither is applicable
with igb>0. At the same time, in addition, it is stated in the Manual
that "ibelly option does not provide any significant speed advantage".
Already in 2008 David Case mentioned the paper "Application of the
Frozen Atom Approximation to the GB/SA Continuum Model for Solvation
Free Energy" from Guvench et al. (2002), where certain approximations
were introduced (but not with the AMBER suite) to freeze a part of the
system, which was not important for the studied region. Is there maybe
anything similar available for AMBER at the moment (I'm running AMBER14)?
I'm very new to the use of REMD in AMBER so maybe I overlooked already
existing answer to my question in the Mailing List, I'm sorry in this case.
Thanks and best wishes,
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 Sep 08 2015 - 01:00:04 PDT
