AMBER Archive (2004)

Subject: Re: AMBER: freezing atoms in impliciti solvent

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Aug 24 2004 - 12:54:58 CDT

freezing part of the system in GB is not as trivial as with non-GB
calculations, since one still needs to calculate
descreening effects between frozen atoms so that the effective Born
radii are known for the frozen atoms
when calculating their interaction with the moving part. This has been
addressed in the literature
(Still, J. Comp. Chem 2002). There may be other reasons as well that
others may point out,
but you could probably modify the code to get it working.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Sergio E. Wong wrote:

>Dear Amber users;
>
> I am trying to simulate the dynamics of a section of a protein (say a
>8 A sphere within a given point). For computational efficiency, I also
>want to use the GB/SA implementation in amber. I noticed that the manual
>says IBELLY =1 is not possible for igb>0 (Amber 7 manual). I wonder if
>there is any way around this. I realize I could impose a harmonic
>restraint using NTR=1, however, that would not reduce the number of force
>calculations in my simulation and thus defeat the point.
>
>Any suggestions?
>
>Thanks in advance
>
>-Sergio
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