Hi Guys,
Just a few questions regarding toluene set up and run.
Trying to set up toluen 216 molecules:
antechamber -i toluene.mol2 -fi mol2 -o toluene.pdb -fo pdb
antechamber -i toluene.pdb -fi pdb -o toluene.mol2 -fo mol2 -c bcc
parmchk -i toluene.mol2 -f mol2 -o toluene.frcmod
then in tleap
source leaprc.gaff
TOL = loadmol2 toluene.mol2
loadamberparams toluene.frcmod
BULK = loadpdb TOLUENE.pdb
setbox BULK centers
saveAmberParm BULK TOLUENE_216.prmtop TOLUENE_216.inpcrd
quit
then running min, eql, and production. Running production gives
NSTEP = 177900 TIME(PS) = 357.800 TEMP(K) = 329.83 PRESS = -40.7
Etot = 3895.3213 EKtot = 2619.1565 EPtot = 1276.1648
BOND = 570.2390 ANGLE = 1053.1037 DIHED = 688.1559
1-4 NB = 961.6047 1-4 EEL = -963.6260 VDWAALS = -1601.8145
EELEC = 568.5021 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 199.0413 VIRIAL = 234.9427 VOLUME = 40887.3038
Density = 0.8082
Ewald error estimate: 0.2108E-04
Questions are
Why is EPtot positive?
Why are the Angle, Bond, and DIHED so huge ?
What is wrong with the set up?
Thank you so much in advance for any help.
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Received on Mon Feb 29 2016 - 18:30:02 PST
