Hi,
We are learning TI computation for protein-ligand binding using pmemd of
amber14. We used 3-step protocol ((1)switch charge off, (2) vdw
transformation, (3)switch charge back on) to compute Delta Delta G of two
ligand binding with the same protein.
The results of the vdw transformation are summarized below:
Delta G (Complex) Delta G(Solution)
-1.6746+-4.7307 -0.4455+-4.0797 (pmemd of amber14: ligand charge: BCC
charge!)
-10.8895+-6.0608 -13.1352+-5.4417 (sander of amber11: ligand charge: RESP
charge!)
Because we used BCC charge this time for pmemd, we have not used RESP charge
yet. But, in the vdw transformation, the charges are off. Therefore, I think
the Delta G (not Delta Delta G) should be similar. But they differ by ~10
kcal/mol in the complex and solution computations, respectively. The Delta
Delta G¡¦s are indeed in the similar range.
Any advice/suggestions are appreciated.
We also found a typo, I think, in the output file. As shown below, it should
be ¡§A V E R A G E S O V E R 600000 S T E P S¡¨ instead of 3000 S T E P
S.
| TI region 1
A V E R A G E S O V E R 3000 S T E P S
NSTEP = 600000 TIME(PS) = 1460.000 TEMP(K) = 300.09 PRESS =
-116.9
Etot = -9653.6227 EKtot = 2273.8284 EPtot =
-11927.4511
BOND = 7.9001 ANGLE = 14.6115 DIHED =
14.3599
1-4 NB = 12.6016 1-4 EEL = 0.0000 VDWAALS =
1754.7994
EELEC = -13731.7236 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 1126.9247 VIRIAL = 1224.9449 VOLUME =
38839.1790
Density =
0.9804
DV/DL = -3.5789
Would like to take this opportunity to thanks many in Amber community,
particularly code developers!
Thanks very much.
Ying-Chieh
Ying-Chieh Sun, Professor of Computational Chemistry
Chemistry Department
National Taiwan Normal University
Taipei, Taiwan 11617
Tel: +886-2-7734-6215
Fax: +886-2-2932-4249
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Received on Wed May 14 2014 - 03:30:02 PDT
