[AMBER] frozen geometry setting?

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 30 Aug 2016 14:32:09 +0000

Dear Amber List experts,

I need in the first step of energy minimization
to hold frozen geometry of protein and membrane (residues 1 to 1097).
I have applied minimization with restraints (see script below).
Unfortunately, protein residues change their geometry significantly.
I suggest that applying frozen geometry for protein and membrane
could be a solution. Unfortunately, I failed to find in Amber manual
and in its tutorials how to define frozen geometry for the target system subsets.
I would appreciate any advises what changes must be used in the script below
for the frozen geometry settings.

Thank you,

initial minimisation: solvent
  imin = 1, iwrap = 1,
  maxcyc = 40000,
  ncyc = 5000,
Hold the protein and membrane fixed
ntr=1, restraintmask=':1-1097',

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Received on Tue Aug 30 2016 - 08:00:02 PDT
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