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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Received on Tue Aug 25 2015 - 11:00:03 PDT
