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 - 11:30:03 PDT
