Dear Amber Users,
I have to pull the ligand from protein in z-direction to record the force
in each step. I have tried the following restraint code.
I Need suggestion to define the constant velocity code.
The distance between COM of protein and COM of ligand in the equilibrated
structure is 8.138 Angstrom.
And I want to pull the ligand to 30 Angstrom from its initial position,
How to define the r1, r2, r3 and r4 distance variables?
The restraint file is as follows.
####
&rst
iat=-1,-1, || to define the group of distance
r1=,
r2=,
r3=,
r4=,
rk2=,
rk3=,
iresid=0,
fxyz=0,0,1, || dierection_of_pulling
outxyz=1, ||details to print
igr1=ligand_atoms,
igr2=protein_atoms,
/
2. I tried the following also,
I have selected one atom closer to COM of protein and another one near to
COM of ligand. Pulled the ligand using the following input&restraint file.
Simulation is running without any error.
###############
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=250000, ntt=3, gamma_ln=1.0,
temp0=303.0,
ntpr=1000, ntwr=500000, ntwx=1000,
dt=0.002, ig=-1,
ntb=2, cut=10.0, ioutfm=1, ntxo=2,
nmropt=1, ntp=1, jar=1,
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END', /
DISANG=COM_pull.RST
DUMPAVE=05_Pull_dist.dat
LISTIN=POUT
LISTOUT=POUT
#############
&rst
iat=4311,3473,
r2=8.138,
rk2=100,
r2a=33.138,
##########and output file looks like#############
8.13800 9.23098 -524.62950 0.00000
8.21800 8.21329 2.25910 -0.30317
########
Why the in force is negative value?
Then How I can correlate with ligand affinity or how strong the ligand
bound with protein?
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Received on Sun Sep 02 2018 - 10:00:03 PDT
