Dear amber committee
I am using the ff02 polarizable force field with TIP3P water model, the
leapin is :
source leaprc.ff02polEP.r1
pep = sequence{NSER ALA ALA GLU ALA TYR ALA LYS ARG ILE ALA GLU ALA MET
ALA LYS CGLY}
solvatebox pep TIP3PBOX 10.0
addions pep Cl- 0
savepdb pep peptide_linear_wat.pdb
saveamberparmpol pep pep.top pep.crd
quit
The input file is attached
when minilization, the outfile is as follows:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -8.0938E+04 1.0479E+01 5.6961E+02 H 95
BOND = 14482.8030 ANGLE = 29.6186 DIHED = 126.5720
VDWAALS = 24052.6486 EEL = -87094.7592 HBOND = 0.0000
1-4 VDW = 80.6514 1-4 EEL = 882.2751 RESTRAINT = 0.0000
EPOLAR = -33497.5349
Dipole convergence: rms = 0.773E-04 temperature = 0.00
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -9.9285E+14 8.2626E+17 1.0696E+20 O 995
BOND = 27217.7852 ANGLE = 43.6487 DIHED = 133.3883
VDWAALS = 27835.5582 EEL = -4418425.3325 HBOND = 0.0000
1-4 VDW = 75.0408 1-4 EEL = 888.0260 RESTRAINT = 0.0000
EPOLAR = *************
Dipole convergence: rms = 0.349E+12 temperature = 0.00
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -8.6779E+20 7.9955E+25 7.1880E+27 O 995
BOND = 27217.8050 ANGLE = 43.6487 DIHED = 133.3883
VDWAALS = 27835.5644 EEL = ************* HBOND = 0.0000
1-4 VDW = 75.0408 1-4 EEL = 888.0260 RESTRAINT = 0.0000
EPOLAR = *************
Dipole convergence: rms = 0.357E+18 temperature = 0.00
then the restart in heat as follws:
NSER
12193 0.8900000E+02
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Can you tell how to modify the input file? Thank you very much
lily
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Received on Sat Jul 10 2010 - 00:30:03 PDT
