be careful with your force constants- they need to be quite large. from the
manual: Note that angle positions are specified in degrees, but
*force* constants
are in *radians*,
On Wed, Oct 16, 2013 at 1:23 PM, Brian Radak <radak004.umn.edu> wrote:
> 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
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Wed Oct 16 2013 - 11:00:02 PDT
