AMBER Archive (2008)

Subject: AMBER: Variable PBCAL values in MM-PBSA calculations

From: Daniel Oehme (
Date: Mon Dec 01 2008 - 17:45:23 CST


I am running some MM_PBSA calculations using AMBER 10 and have been
getting some highly variable PBCAL values depending on what water type
I assign a structural water molecule in the active site to be. The
issue comes when trying to use the TIP5P water type. For TIP3P
simulations I get the following results:
                    Complex SD Receptor SD
Ligand SD Delta SD
PBCAL -2066.21 39.76 -2103.88 39.57
-45.30 1.39 82.96 7.24

while for the TIP5P I get:
                    Complex SD Receptor SD
Ligand SD Delta SD
PBCAL -2549.08 369.70 -2188.62 295.53
-45.77 1.23 314.69 243.66

Please note that two different simulations were run to get these
results. As can be seen, the Complex and Receptor have extremely high
SD's but the Ligands values are fairly similar. If however I run the
MM-PBSA calculations without the structural water molecules in the
TIP5P simulation I get the following results:
                   Complex SD Receptor SD
Ligand SD Delta SD
PBCAL -1982.99 66.10 -2024.60 66.13
-45.77 1.23 87.38 4.61

I have also run a calculation on the TIP5P simulation by making the
structural water molecule TIP3P instead of TIP5P and got these
                   Complex SD Receptor SD
Ligand SD Delta SD
PBCAL -1982.75 66.07 -2027.20 65.99
-45.77 1.23 90.23 4.65

As can be seen, the last two sets of results give SD's are a lot lower
in this case yet still a bit higher than in the inital TIP3P
simulations. My theory is that the PBCAL calculations are getting
confused by the extra points (EP) that are included in the TIP5P water
model compared to TIP3P. My question is can anybody think of a reason
as to why the PBCAL values would get confused with the EP's and how I
can change the setup of the calculation to be able to run the MM-PBSA
calculations with a TIP5P structural water molecule?

MM-PBSA calculations were run without a solvent sphere and with
standard input except for fillratio which was increased to 4.

Daniel Oehme
PhD Student
La Trobe University
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