What I don't understand is why does "cavity_offset" defaults to 0.000
for inp=1 ?
From the original paper by Sitkoff et al 2004 (Barry Honig's group) it
should be 0.86 ... Or ? Am I missing something ?
Vlad
On 03/24/2014 04:41 PM, Jason Swails wrote:
> 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
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Mon Mar 24 2014 - 09:00:03 PDT
