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
> _______________________________________________
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> 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
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Received on Wed Oct 16 2013 - 08:00:03 PDT
