On Tue, Aug 30, 2016, Michael Shokhen wrote:
> I have applied minimization with restraints (see script below).
> Unfortunately, protein residues change their geometry significantly.
Your restraints were never applied (see below), which should have been
clear from the mdout file.
>
> 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,
> /
The above line ends the namelist; all further cards are ignored.
> ntr=1, restraintmask=':1-1097',
> restraint_wt=5000.0
Put the above two lines *into* the &cntrl namelist (before the "/" line.)
Consider using a restraint_wt two orders of magnitude smaller than what you
have here.
...good luck...dac
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Received on Tue Aug 30 2016 - 10:30:03 PDT
