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
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Received on Wed Oct 16 2013 - 10:00:18 PDT
