Dear Amber experts,
I am new Amber user. I am entering this forum seeking
your advice.
My problem is my protein jumping out of the water box,
which is a truncated waterbox216. I use Amber7 and
force field 99.
After minimization, my protein is well surrounded by
water. I continued to heat up my system to 305K. This
is my input file:
&cntrl
imin=0, nmropt=1
nstlim=10000, dt=0.001,
ntpr=50, ntwr=1000, iwrap=1, ntwx=200,
ntf=2, ntc=2, ntb=1,
ntt=1,
&end
&wt type='TEMP0', istep1=0,istep2=1000,value1=0.0,
value2=5.0, &end
&wt type='TEMP0', istep1=1001,istep2=5000,value1=5.0,
value2=100.0, &end
&wt type='TEMP0',
istep1=5001,istep2=10000,value1=100.0,
value2=305.0, &end
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.5,
value2=0.5, &end
&wt type='TAUTP',
istep1=5001,istep2=10000,value1=0.5,
value2=0.1, &end
&wt type='END' &end
I haven’t known how to use Moil-view so I make a pdb
file from trajectory output file. My protein already
jumped out after the first time frame (after 200fs).
About 1/4 of my protein is outside waterbox.
Second, I tried to change some features. This is my
new input file:
&cntrl
imin=0, nmropt=1
nstlim=50000, dt=0.001,
ntpr=50, ntwr=1000, iwrap=1, ntwx=200,
ntf=2, ntc=2, ntb=1,
ntt=1, nscm=10, tautp=0.1
&end
&wt type='TEMP0', istep1=0,istep2=10000,value1=0.0,
value2=5.0, &end
&wt type='TEMP0',
istep1=10001,istep2=25000,value1=5.0,
value2=100.0, &end
&wt type='TEMP0',
istep1=25001,istep2=50000,value1=100.0,
value2=305.0, &end
&wt type='END' &end
My protein still jump out.
Third, I tried to heat up my protein using temperature
ramp with the temp at the beginning already 305K and
everything restrain. Next, I would losen some restrain
atoms.
# Equilibration of solvent and hydrogens
&cntrl
imin=0, nstlim=2500, dt=0.002,
ntx=1, irest=0, ntr=1,
ntpr=50, ntwx=200, ntwr=2500, iwrap=1,
ntf=2, ntc=2, tol=0.00000001, ntb=2,
tempi=305.0, temp0=305.0,
ntt=1, tautp=0.5,
pres0=1.0, ntp=1, taup=0.6,
&end
Group input for amino acid restrains
50.0
FIND
* * M *
* * B *
* * S *
* * 3 *
SEARCH
RES 1 468
END
Group input for ion/substrate restrains
50.0
RES 469
END
END
Just after this running, I see my protein is already
out of the water box.
What is happening? Why iwrap=1, small NSCM or restrain
almost every atom doesn’t help? My protein always goes
out and the water box deformed.
I greatly appreciate any advice. Please help
Best wishes,
Lich Nguyen
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Received on Thu Oct 24 2002 - 02:45:45 PDT
