Hi AMBER users,
I am trying to construct an adiabatic map for an enzyme ligand complex in
which the ligand binds covalently to a residue in the protein. I am
restraining a distance between a ligand atom and a protein atom over a
range. My input file for minimization looks like this
Initial minimisation
&cntrl
imin=1, maxcyc=2000, ncyc=1000,
cut=12, ntb=1, igb=0, nmropt=1,
&end
&wt
type='END',
&end
DISANG=RST-8.dist
and the distance file is
#
# 123 CYM SG 432 UNK C38 1.0 5.3 &rst
ixpk= 0, nxpk= 0, iat=1937,6833, r1= 0.50, r2= 1.00, r3= 5.30, r4= 5.80,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
When I run the minimization I only get zero values for the restrain like
this:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.2114E+05 2.2113E+01 1.2152E+03 O 20311
BOND = 1257.6726 ANGLE = 2422.4741 DIHED =
4450.7597
VDWAALS = 13925.5850 EEL = -161068.9140 HBOND =
0.0000
1-4 VDW = 1614.9207 1-4 EEL = 16259.9956 RESTRAINT =
0.0000
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
What could have gone wrong?
Many thanks,
Mahmood Jasim
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Received on Thu Sep 18 2014 - 05:00:08 PDT
