Using cpptraj to evaluate the mask, that is a great idea.
should actually be:
':317.O | (!:WAT & !.H=)'
!.WAT & !.H= doesn't cover the water oxygen...
devils in the details.
As always, thanks Jason!
On Wed, Jun 10, 2015 at 2:09 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> Sorry for the blank email. I tried to click something *not* send and
> missed.
>
> On Wed, Jun 10, 2015 at 1:48 PM, Jonathan Gough <
> jonathan.d.gough.gmail.com>
> wrote:
>
> > Hi All,
> >
> > I want to put restraints on all heavy protein atoms AND the oxygen of a
> > single water.
> >
> > I thought I proved this worked in a test case, but from what I can tell,
> it
> > didn't work in my production.
> >
> > I "believe" the line should be:
> >
> > ntr=1, restraintmask=':317.O | (!.WAT & !.H)', restraint_wt=25
> >
>
> Assuming that residue 317 is the water you want to restrain, yes, this is
> it.
>
>
> >
> >
> > yes?
> >
> > The full production input is:
> >
> > &cntrl
> > imin = 0, nstlim = 10000000, dt = 0.002,
> > irest = 1, ntx = 5, ig = -1,
> > tempi = 300.0, temp0 = 300.0,
> > ntc = 2, ntf = 2, tol = 0.00001,
> > tautp = 1.0, taup = 1.0,
> > ioutfm = 1
> > ntwx = 500, ntwe = 0, ntwr = 500, ntpr = 500,
> > cut = 8.0, iwrap = 1,
> >
>
> I'd suggest turning iwrap off for restrained simulations.
>
>
>
> > ntt =3, gamma_ln = 1.0, ntb = 1, ntp = 0,
> > nscm = 0,
> > ntr=1, restraintmask=':317.O | (!.WAT & !.H)', restraint_wt=25
> > &end
> >
>
> You can use cpptraj or ParmEd to evaluate your mask and print out what
> atoms are present. If you're trying to verify that it selects the atoms
> you intend to select, I would recommend doing that.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jun 10 2015 - 12:30:04 PDT
