Dear Amber
I would like to bring the ligand from far distance from the receptor to the
surface of the receptor. The atoms that I have selected on the ligand and
on the receptors are now 22.5 angstrom apart. I need to pull the ligand to
near the surface of the receptor, which is 16.2 angstrom from the receptor
fixed atom. I have used the following parameters to run the simulation. I
have enclosed restrain file too. In restrain for these kind of simulation
the ifvari=1 should be applied. When I see the distance change between the
two points it is not linear it jumps randomly. How I can control the
variables to make the force so that the distance decrease with respect to
time is linear.
I have used the following MD run script
molecular try 1
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0, nmropt=1,tautp=1.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 200000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwe = 1000,
iwrap=1,
/
&wt type='REST', istep1=0,istep2=200000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=rst.bb
/
restrain file
# DIST REST 1372 CA ----- 2024 C3
&rst
iat=1372,2024, nstep1=0, nstep2=100000, ifvari=1,
r1a=16.2, r2a=18.3, r3a=20.3, r4a=22.5, rk2a=0.01, rk3a=0.01,
&end
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Received on Mon Jan 25 2016 - 10:30:04 PST
