I have not used setbox BULK in the manner that you are doing. One option
you might try is to use the AddToBox mini program I wrote a few years back
in $AMBERHOME/bin. Just run the program with no arguments to see what it
takes, but with your pdb of toluene all you'd need is something like -c
TOLUENE.pdb -a TOLUENE.pdb -na 215 then specify your box parameters. Make
sure to check that all of the toluene is being added, and use -V 1 or
increase the initial box size if not.
My feeling is that the setup is fine, though. All of the angles, bonds,
and dihedrals are probably at equilibrium when toluene is in its simplest,
unstretched, flat conformation. Any perturbations, as are bound to happen
with temperature, are going to perturb that state and add to EPtot. The
angle, bond, and dihedral energies may not be that large for 216 molecules
jiggling around at 330K--2.5 kcal/mol and 5 kcal/mol per 86 MW molecule
doesn't seem unreasonable.
HTH,
Dave
On Mon, Feb 29, 2016 at 9:02 PM, Starovoytov, Oleg <ostarovo.central.uh.edu>
wrote:
> 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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>
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Received on Mon Feb 29 2016 - 19:30:04 PST
