Hello!
Does amber9 support solvating only a small portion of the protein (say
active site with ligand) with a TIP3PBOX water cap (25A) around it, using
igb=10? or does the entire protein have to be within the cap?
I am working on a dimer with a ligand, a system of ~6000 atoms. If I try to
use explicit solvent (using a water box), a mere 8A box hikes the number to
almost 90k atoms, which is too big for our computer system. I tried to run
the water cap option with the following min and equil steps which ran fine,
on trying the production run, the md output gives errors of "vlimit
exceeded". Earlier I tried using the implicit solvent option of igb=2,
gbsa=1, but does not work for my system, one of the subunits of the dimer
seem to move away from the other quite rapidly. So, am I missing any options
that I could try and also what am I doing wrong here?..
min.in
&cntrl
imin=1, maxcyc=5000, ncyc=1000, ntb=0, ntpr=20, scee=1.2, nsnb=25,
ntmin=2, cut=12,
&end
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 -1.2772E+04 2.7340E-01 4.6052E+00 O 10911
BOND = 564.0388 ANGLE = 1303.0728 DIHED =
5820.9651
VDWAALS = -4605.3428 EEL = -47067.8395 HBOND =
0.0000
1-4 VDW = 2088.6990 1-4 EEL = 29124.6525 RESTRAINT =
0.2275
EAMBER = -12771.7542
equil.in
&cntrl
imin=0, irest=0, ntx=1, ntb=0, cut=12, ntc=2, scee=1.2,
ntf=2, tempi=0.0, temp0=300.0, ntt=1, taup=0.1, dtemp=2.0, ntp=0, nsnb=25,
nstlim=20000, dt=0.002, ntpr=250, ntwx=250, ntwr=1000,
&end
A V E R A G E S O V E R 5000 S T E P S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 237.81 PRESS =
0.0
Etot = -5968.9244 EKtot = 5828.3659 EPtot = -
11797.2903
BOND = 1192.5247 ANGLE = 3215.4731 DIHED =
6228.2326
1-4 NB = 2200.3827 1-4 EEL = 29157.2263 VDWAALS = -
5406.3059
EELEC = -41625.3623 EGB = -9040.6615 RESTRAINT =
2149.6171
ESURF= 131.5828
EAMBER (non-restraint) = -13946.9074
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 74.91 PRESS =
0.0
Etot = 3736.7361 EKtot = 1835.9481 EPtot =
1902.7262
BOND = 356.7281 ANGLE = 756.1285 DIHED =
177.5090
1-4 NB = 57.5145 1-4 EEL = 39.3693 VDWAALS =
61.2788
EELEC = 339.9597 EGB = 328.2173 RESTRAINT =
526.3146
ESURF= 0.3270
EAMBER (non-restraint) = 1376.4116
Now, the troublesome MD run:
&cntrl
ntx=5, irest=1, imin=0,
ntpr=500, ntwx=500, ntwr=5000,
nstlim=100000, dt=0.001,
ntt=1, tempi=300.0, temp0=300.0, tautp=0.1,
igb=10, ntb=0, cut=0, fcap=10.0, ivcap=0,
ntc=2, ntf=2, tol=0.000001,
&end
RESULTS
vlimit exceeded for step 29; vmax = 27.5043
vlimit exceeded for step 30; vmax = 93.7706
vlimit exceeded for step 31; vmax = 38.9037
vlimit exceeded for step 32; vmax = 80.5579
vlimit exceeded for step 33; vmax = 137.4696
Thanks, any help will be much appreciated!
--
-Rima
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Received on Wed Oct 17 2007 - 06:07:33 PDT
