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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Received on Tue Oct 15 2013 - 21:00:02 PDT
