Daniel,
Just my 2c ...
If you use radiopt=1, I think the radius optimized for TIP3P may be too
small for TIP5P, i.e. the two extra points are too close to the surface of
the solvent probe sphere boundary, which may cause highly fluctuating PB
energies.
Maybe use of radiopt=0 could resolve the problem since the radius for the
two hydrogen atoms (1.30A) may be large enough to cover the two EP's.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Daniel Oehme
Sent: Monday, December 01, 2008 3:45 PM
To: amber
Subject: AMBER: Variable PBCAL values in MM-PBSA calculations
Hi,
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
results:
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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Received on Fri Dec 05 2008 - 18:25:33 PST
