Hello,
I have used amber8 for a 10ns MD simulation of a protein with a peptide
ligand. I am using the MM-PBSA approach to calculate binding energies. Prior
to that I have used ptraj to strip off the water molecules and produce a
sample of 3000 frames. I have obtained the solvent free trajectory file
without box information using the command "nobox". For the MM-PBSA I have
also used topology files of the protein/peptide alone without the solvent
for the receptor, the ligand and the complex alike.
Here are some average values after 10ns (from sander):
NSTEP = 1000000 TIME(PS) = 10348.000 TEMP(K) = 299.97 PRESS =
1.0
Etot = -71620.5802 EKtot = 17663.2402 EPtot =
-89283.8204
BOND = 471.5498 ANGLE = 1249.2446 DIHED =
1032.0699
1-4 NB = 570.5820 1-4 EEL = 7585.9984 VDWAALS =
10987.3725
EELEC = -111180.6375 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 7931.6683 VIRIAL = 7925.6129 VOLUME =
290168.8089
Density =
1.0126
No non-standard residues were used. All initial files were prepared in xleap
with the ff94 and no error message was given. The overall charge of the
complex is 0. Also the trajectory viewing did not show any obvious glitches,
like very close contacts between atoms.
For the MM-PBSA anaylis the standard input file was used as given in the
examples. Right from the beginning of the calculations I am getting big vdw
energies:
MM
GB
PB
MS
1
BOND = 458.3980 ANGLE = 1273.1135 DIHED =
1034.8045
VDWAALS = -1181.8598 EEL = -11779.2769 EGB =
-2284.3446
1-4 VDW = 581.0556 1-4 EEL = 7515.1325 RESTRAINT =
0.0000
corrected reaction field energy: -4753.964000
surface area = 9755.332
2
BOND = 4523480.6293 ANGLE = 223348.6443 DIHED =
7574.9785
VDWAALS = ************* EEL = -5505.6505 EGB =
-2968.0169
1-4 VDW = ************* 1-4 EEL = 529.2179 RESTRAINT =
0.0000
corrected reaction field energy: -7557.501000
surface area = 10160.164
3
BOND = 5080825.5589 ANGLE = 211012.6282 DIHED =
7111.4286
VDWAALS = ************* EEL = -4468.8932 EGB =
-2793.3557
1-4 VDW = ************* 1-4 EEL = 1132.4822 RESTRAINT =
0.0000
corrected reaction field energy: -7845.509000
Any suggestion on why Bond, vdw and angle values have exploded would be very
helpful.
Regards,
John
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Received on Sun Jul 03 2005 - 22:53:01 PDT
