Dam,
Can you run your sander by hand after turning on npbverb=1? Please
email Qin off the list your input and output files from both Amber10
and Amber11. We'll be happy to take a look of your calculations.
In general, we want to use the best default options at the time of
each release so your observances are quite reasonable.
All the best,
Ray
On Thu, Jun 7, 2012 at 9:09 AM, Damodaran, Komath
<Komath.Damodaran.elan.com> wrote:
> 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 - 10:00:04 PDT
