Hello,
I am trying to minimize my protein + water system, where protein is
represented by ff02 polarizable force field and the waters are with POL3
force field.
I am using AMBER8 in a dual processor linux machine.
My commands in xleap was
WAT=PL3
loadamberparams frcmod.pol3 (this 2 lines are for the waters present in
the PDB file)
xx = loadpdb xx.pdb
solvateBox xx POL3BOX 10
addions2 xx Cl- 6
saveamberparmpol xx xx.top xx.crd
Xleap saved the top and crd files.
However, when I run a minimization with sander with the following input file:
&cntrl
IMIN=1,
NCYC=100,
maxcyc=500,
IPOL=1
NTR=0
&end
I get something like this
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.7510E+19 1.0640E+18 2.1944E+20 HE21 30
BOND = 2218.1501 ANGLE = 827.2355 DIHED = 1791.8357
VDWAALS = 122128.0995 EEL = ************* HBOND = 0.0000
1-4 VDW = 723.0874 1-4 EEL = 10994.1160 RESTRAINT = 0.0000
EPOLAR = ************* ETHREEB = 0.0000
Dipole convergence: rms = 0.124E+08 temperature = 0.00
NSTEP ENERGY RMS GMAX NAME NUMBER
50 1.0814E+20 1.0607E+17 2.1993E+19 HE21 30
BOND = 3562.1325 ANGLE = 1108.8050 DIHED = 1804.7233
VDWAALS = 122086.6980 EEL = ************* HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 10796.1395 RESTRAINT = 0.0000
EPOLAR = ************* ETHREEB = 0.0000
Dipole convergence: rms = 0.108E+09 temperature = 0.00
and eventually it crashes.
If I replace POL3 with TIP3P (i.e. ff02 + TIP3P), it works fine.
Can someone please help me? Thanks.
Pradipta
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Received on Wed May 17 2006 - 06:07:09 PDT
