Hi Bill,
Thanks for your suggestion. In fact, I had compared the mdout files from
both runs and
whatever input variables that sander spits out at the beginning of mdout
of both runs do match.
That's why I felt like I had come to a dead end!
Thanks again,
Dam
>As far as I can remember, I do not recall any changes in default PB
>parameters within MMPBSA.py. However, the defaults in the pbsa routines
>called by sander may have changed between versions. You should be able
to
>check the mdout files produced by MMPBSA.py. Prior to the energy
>calculations, the mdout file should contain a list of all the input
>variables used for the sander calculation. If you compare the output
files
>from sander in Amber 10 and Amber 11, any differences should be the
cause
>of any discrepancies you see in the results. And since EPB is the only
>value that is different, you should only have to compare the PB input
>variables listed in those files.
>I hope that helps.
>-Bill
>On Wed, Jun 6, 2012 at 11:18 AM, Damodaran, Komath <
>Komath.Damodaran.elan.com> wrote:
>> Hi,
>>
>> I have a puzzle with MMPBSA calculations using Sander in Amber10 and
>> Amber11 versions.
>> I am running MMPBSA calculations on a moderate size protein:ligand
>> complex (about 300AAs).
>> When I use the same topology, trajectory and inpcrd files along with
>> the same mdinp options, the EPB value is lower in Amber 10 by about
>> 12kcal/mol. All other numbers (vdw, Coulomb term, cavity term) match
>> between Amber 10 and Amber 11.
>> I am wondering if any of the default parameters have changed between
>> versions 10 and 11.
>> Here are the input options that I use.
>
>> &cntrl
>>
>> nsnb=99999, ntb=0, cut=999.000000, imin=5,igb=10,
>>
>> /
>>
>> &pb
>>
>> sprob=1.400000, maxitn=1000, fillratio=4.000000
>>
>> radiopt=0, npopt=1, dbfopt=1, cavity_surften=0.005240,
>>
>> /
>>
>> END
>>
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Received on Thu Jun 07 2012 - 09:30:03 PDT
