No. In that case you would want something like r1=0.0 r2=9.0 r3=9.0
r4=509.0.
FYI. Just setting "r0 = 9.0" will give those exact settings (sander only).
Regards,
Brian
On Wed, Oct 16, 2013 at 12:38 PM, Nihal Korkmaz <enihalkorkmaz.gmail.com>wrote:
> That was a typo, i meant both force constant for the torsional restraint
> to be 1000 so that I can keep the two arginines in the desired orientation.
>
> The problem was the dihedral restraint was not working. Now that I
> further increased the torsional rk2 and rk3, it is working better:
> &rst
> ixpk=0, nxpk=0, iat=16,41, r1= 7.5, r2= 8.0, r3= 10.0, r4= 10.50,
> rk2=100.0, rk3=100.0, ir6=1, ialtd=0,
> &end
> &rst
> iat=14,16,41,39
> r1=175.0, r2=180.0, r3=180.0, r4=185.0,
> rk2=5000.0, rk3=5000.0,
> &end
>
> However, as you said the distribution of distances is not harmonic.
> After checking the manual and the tutorial again, if I change to r1=
> 1.30, r2= 1.80, r3= 9.00, r4= 9.50 i suppose it would keep my distance
> around 9 with a harmonic potential. Am i right?
>
> Thank you,
> Nihal
>
> On 10/16/2013 9:30 AM, Brian Radak wrote:
> > Hi Nihal,
> >
> > Can you elaborate on your "problems"? What exactly isn't happening as
> > expected? Is AMBER giving an error or is the dynamics just not as you
> > expected?
> >
> > That being said, your restraints look a bit unusual to me. Did you intend
> > these to be harmonic? If so, your values for r1 and r4 seem like
> > potentially poor choices. I assume you've read the manual describing the
> > flat bottom well restraint form employed by nmropt. Also, did you mean
> for
> > the dihedral force constants to be different?
> >
> > Regards,
> > Brian
> >
> >
> > On Tue, Oct 15, 2013 at 11:44 PM, Nihal Korkmaz <enihalkorkmaz.gmail.com
> >wrote:
> >
> >> Dear all,
> >>
> >> I am trying to get the PMF profile for two Arginines restricted on the
> >> same plane (I added a torsinal NMR constraint for NE-CZ-CZ'-NE' atoms)
> >> with the reaction coordinate being the distance between the two CZ
> >> atoms. However, i am having problems in keeping the Arginines on the
> >> same plane.
> >>
> >> This is my input file for equilibriating the system:
> >> &cntrl
> >> imin = 0, ntx = 1, irest = 0,
> >> ntpr = 10, ntwr = 50000, ntwx = 0,
> >> ntf = 2, ntc = 2, cut = 12.0,
> >> tol=0.000001,
> >> ntb = 2, nstlim = 500000, dt = 0.001,
> >> tempi=0.0, temp0 = 300.0, ntt = 3,
> >> gamma_ln =20.0,
> >> ntp = 1, pres0 = 1.0, taup = 5.0,
> >> nmropt = 1, ioutfm=1,
> >> &end
> >> &wt
> >> type='DUMPFREQ', istep1=50,
> >> &end
> >> &wt
> >> type='END',
> >> &end
> >> DISANG=restraintfile
> >> DUMPAVE=dihedral_dist.out
> >>
> >>
> >> with restraintfile:
> >> &rst
> >> ixpk=0, nxpk=0, iat=16,41, r1= 7.5, r2= 8.0, r3= 10.0, r4= 10.50,
> >> rk2=100.0, rk3=100.0, ir6=1, ialtd=0,
> >> &end
> >> &rst
> >> iat=14,16,41,39
> >> r1=175.0, r2=180.0, r3=180.0, r4=185.0,
> >> rk2=100.0, rk3=1000.0,
> >> &end
> >>
> >> I appreciate any suggestions regarding this issue
> >>
> >> Thanks,
> >> Nihal
> >>
> >> --
> >> E. Nihal Korkmaz
> >> UW-Madison, Biophysics Program
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> --
> E. Nihal Korkmaz
>
> Research & Teaching Assistant
> UW-Madison, Biophysics Program
> Member of Qiang Cui Lab
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone: 608-265-3644,
> Email: korkmaz.wisc.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Wed Oct 16 2013 - 10:30:03 PDT
