Dear Amber users
I did SMD of protein ligand complex (20A from the initial position), and
in the result file the work for pulling the ligand is keep on incresing as
regard with the distance!,
I am expecting plot such the force will increase while pulling the ligand
out from the cavity then decrease after the ligand came out of the cavity.
Am I doing correctly? i still need a clarification about this!
I have pasted the result file and input files am using for pulling the
ligand out from protein.
"""
8.13800 9.23098 -218.59562 0.00000
8.21800 8.25037 -6.47449 -0.54583
8.29800 8.31760 -3.92022 -0.88007
8.37800 8.47082 -18.56317 -1.00396
8.45800 8.50562 -9.52336 -1.24856
8.53800 8.56110 -4.61905 -1.45729
............
26.93800 26.99166 -10.73237 54.68420
27.01800 26.99442 4.71645 54.74462
27.09800 27.15913 -12.22665 54.79492
27.17800 27.18728 -1.85637 54.79982
27.25800 27.24111 3.37721 54.89353
27.33800 27.36441 -5.28141 54.91381
27.41800 27.40588 2.42494 55.05123
27.49800 27.46560 6.47983 55.19436
27.57800 27.49030 17.54008 55.16678
27.65800 27.68766 -5.93276 55.14094
27.73800 27.71692 4.21613 55.02136
27.81800 27.78315 6.97099 55.08781
27.89800 27.85140 9.32058 55.03641
27.97800 27.96085 3.42948 55.11920
28.05800 28.11506 -11.41155 55.15004
""""""
and i have used the input parameters as
############
pulling
&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=3, csurften=3, gamma_ten=0.0, ninterface=2, jar=1,
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END', /
DISANG=COM_pull.RST
DUMPAVE=05_Pull_dist.dat
LISTIN=POUT
LISTOUT=POUT
/
/
&ewald
skinnb=3.0,
/
#########
.rst file
&rst
iat=4311,3473,
r2=8.138,
rk2=100,
r2a=28.138,
/
############
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Received on Thu Aug 30 2018 - 03:30:02 PDT
