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,
Michael
initial minimisation: solvent
&cntrl
imin = 1, iwrap = 1,
maxcyc = 40000,
ncyc = 5000,
ntb=1,
ntp=0,
ntf=1,
ntc=1,
ntpr=50,
ntwr=2000,
cut=10.0,
/
Hold the protein and membrane fixed
ntr=1, restraintmask=':1-1097',
restraint_wt=5000.0
END
END
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Received on Tue Aug 30 2016 - 08:00:02 PDT
