Hi Jacob,
I haven't used the reaction coordinates often, I hope my suggestion
doesn't sound too trivial.
Maybe the force constant for the plane-point restraints are too weak to
have a significant impact on the simulation.
Achim
> Hi all,
>
> I am having difficulties with simulations pulling a peptide away from a
> surface. The surface is anchored in place with positional restraints
> while the peptide is pulled away from the surface with an increasing
> distance restraint. In order to keep the pulling coordinate roughly
> perpendicular to the surface, a plane-point restraint has been employed.
> Unfortunately, the pulling pathways seem to be quite random, with some
> drawing the peptide nearly parallel to the surface rather than away from
> it.
>
>>From the energies in the output files, it appears that all restraints are
>> being imposed, so it seems that even if jar=1, other NMR restraints can
>> still be applied. Additionally, the defined surface normal is
>> fluctuating from its starting value by no more than 2 degrees. When
>> drawn as a vector in VMD, the surface normal is clearly not in the same
>> direction that the peptide is being pulled. The input file to sander as
>> well as the definitions in the NMR restraints file for the pulling and
>> plane-point restraints are provided at the end of this email.
>
> Is there a fundamental physical flaw in this type of set-up? Or is there
> something wrong with my implementation of the restraints in AMBER? Any
> suggestions would be very much appreciated!
>
> Thanks,
> Jacob
>
> sander input file:
>
> trajectory segment
> &cntrl
> imin = 0, nstlim = 800000, ntwr = 500,
> ntx = 1, irest = 0,
> igb = 5, gbsa = 1,
> saltcon = 0.000000,
> cut = 16.000000, surften = 0.005000,
> tempi = 300.000000, ntt = 3, temp0 = 300.000000,
> tautp = 1.000000, vrand = 500,
> gamma_ln = 2.000000, vlimit = 0.000000,
> ntc = 2, ntf = 2, tol = 1.0d-8,
> dt = 0.002000, nrespa = 2,
> ntb = 0, iwrap = 0, nscm = 510,
> ntpr = 500, ntave = 0,
> ioutfm = 0, ntwx = 500, ntwe = 500,
> ig = -1,
> jar=1,
> nmropt = 1,
> ntr = 1,
> restraint_wt=20.000000,
> restraintmask=':2-12,16,26,30,40,44,54,58,68,72,82,86,96,100-110 |
> (!:2-12,16,26,30,40,44,54,58,68,72,82,86,96,100-110,113-124 & .CA,C,N)',
> &end
> &wt type='DUMPFREQ', istep1=500, &end
> &wt type='END' &end
> DISANG=restraints.txt
> DUMPAVE=dist_force_work.dat
> END
> END
>
> restraint definitions:
>
> #Pulling
> &rst
> iat= -1, 4089,
> iresid=0,
> r2=18.0,
> r2a=50.0,
> rk2=10.0,
> igr1= 9, 500, 3579,
> &end
>
> #Point-plane angle
> &rst
> iat= 9, 500, 9, 3579 4089,
> iresid=0,
> r1=-5, r2=-2.5, r3=2.5, r4=5,
> rk2=1.000000, rk3=1.0000000, ialtd=0,
> &end
>
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>
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Received on Thu Aug 27 2015 - 01:00:03 PDT
