[AMBER] Equilibration of the membrane protein with the restrains

From: James Starlight <jmsstarlight.gmail.com>
Date: Fri, 5 Sep 2014 16:30:45 +0400

Dear Amber users!

I didn't find the protocol of the equilibration of the membrane protein in
the amber tutorial and would like to ask how the restrainsappliedon the
protein atoms should be provided correctly in the input file of the nvt and
npt run. My problem is tha applied restrains on the protein atoms,
providing ntr=1 and -restr frag for the pmemd during the NPT equilibtation
phase there is an artifact with the solvent water which is restrained in
the bottom and upper positions of the bilayer (like in the nvt phase where
no barrostat introduced). I guess it might be due -restr flag provided with
checkpoint file from the previous (nvt) run so the whole system looks
totaly restrained around this state and solvent (water) can't be correctly
equilibrated althought barostat is turned during this phase. Please suggest
me how to restraint protein only for the equilibration not affecting the

Thanksfor help,

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Received on Fri Sep 05 2014 - 06:00:04 PDT
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