On Mon, 2014-03-24 at 12:24 -0300, George Tzotzos wrote:
> Hi Jason,
>
> I have had the same problem (i.e. GB energy of ligand binding (-)ve
> and PB (+)ve. Setting inp=1, throws out the following warnings:
>
> Warning: inp=1 was old default
> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to inp=1 default value: 0.0050
> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to inp=1 default value: 0.000
>
> my mmpbsa input file is:
>
> Input file for running PB and GB
> &general
>
> interval=2, endframe=2000, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> inp=1, istrng=0.100,
> /
>
> Any explanation for this would be much appreciated. What other
> settings are needed to overcome this problem?
The inp=1 and inp=2 nonpolar solvation models are completely different.
In my experience, the inp=2 model is more destabilizing than the inp=1
model (whether for better or worse, I don't know). The default
parameters for the nonpolar solvation method differs depending on which
model you're using, so the warning messages you see is just an
indication that the default inp=2 parameters are being reset to the
default inp=1 parameters (which is consistent with the results you used
to get in previous versions of AmberTools with inp=1).
Of course if you really wanted to compare apples to apples you could
simply substitute the GB nonpolar solvation free energy contribution
into the PB results and recompute your binding free energy that way.
This is equivalent to "using the same nonpolar model" for both GB and
PB.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 24 2014 - 09:00:03 PDT
