Re: [AMBER] Equilibration of the membrane protein with the restrains

From: James Starlight <>
Date: Tue, 9 Sep 2014 09:33:34 +0200

Additional questions:

1) what are the difference between restrain method using

restraint_wt=15.0, restraintmask=':1-361'


Hold protein fixed

RES 1 384

2) is it possible to restrain all protein atoms, or alternatively all
lipids atoms using specific amber mask based NOT on the residue
numbering (e,g to restrain all backbone atoms or all CA etc)?



2014-09-05 14:30 GMT+02:00 James Starlight <>:

> 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
> solvent.
> Thanksfor help,
> James
AMBER mailing list
Received on Tue Sep 09 2014 - 01:00:02 PDT
Custom Search