AMBER Archive (2009)
Subject: Re: [AMBER] implicit solvent MD with fixed residues
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 25 2009 - 14:22:31 CST
On Thu, Dec 24, 2009, Hakan Gunaydin wrote:
> I am trying to run a MD job with some residues allowed to move and
> others fixed. I understand that I need to move the residues that are
> allowed to move to the top of the pdb file.
This is not required if you use NAB, which has flexible support for frozen
atoms in implicit solvent models; (and, unlike sander, you actually save
computation time by not computing frozen-frozen interactions).
How sander really works when both GB and belly are turned on is really quite
complicated, and has changed over the years. You should study the code, and
run some very simple test runs, to make sure you understand what is going on.
For many problems, restraints (ntr=1) are more straightforward to use than
frozen atoms (ibelly=1).
...hope this helps....dac
AMBER mailing list