Hi Debodyuti,
5,000 frames is a big number and might take a while to finish unless the
job is running in parallel. In our experience, dGbind will form a normal
distribution using about 200-500 frames. < 100 frames are probably not
enough. We briefly touch this frame number topic in the Figure 6 of this
article <
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24011/abstract> (J.
Comput. Chem. 2015, DOI: 10.1002/jcc.24011). Feel free to take a look.
HTH,
Pin-Chih
On Tue, Aug 4, 2015 at 8:22 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2015-08-04 at 15:46 +0530, Debodyuti Dutta wrote:
> > hello Amber users,
> >
> > I am facing a strange problem in MM-PBSA and I would like to know if
> there
> > is any solution to it or
> > someone else is also facing the same.
> >
> > In MM-PBSA we use the trajectory protein-ligand trajectory. It write 3
> > output files, namely, _MMPBSA_complex_pb.mdout.0,
> > _MMPBSA_receptor_pb.mdout.0, _MMPBSA_ligand_pb.mdout.0. Problem is that
> the
> > calculation is going on well if there is only 5 frames and the program is
> > writing the .dat files at the end of the calculation; but if there is
> ,lets
> > say, 5000 frames the calculation finishes after writing full
> > _MMPBSA_complex_pb.mdout.0 and not writing the other mdout files.
>
> Are you sure you are giving it enough time to finish? 5000 frames is a
> LOT of frames to analyze -- far too many in my opinion. PB calculations
> can take a long time -- if each one takes ~20 seconds, then 5000 frames
> will probably take more than 2 days (assuming ~40 seconds per frame for
> the complex, receptor, and ligand).
>
> It's possible that there is a bug of some kind, but it will probably be
> difficult to reproduce and detect given that you report it only
> happening for very long calculations. You will probably be better off
> extracting only ~100 to 200 frames for calculation from your trajectory.
> Your answers are unlikely to change by adding more.
>
> > There is
> > no error message of any kind. Although all 3 sets of mdcrd.0, pdb, inpcrd
> > and mdin files are generated by cpptraj before the calculations go
> through
> > Sander. I am using amber14.
>
> What makes you sure that the calculation has finished and is not just
> taking a long time? Another thing you can try is to figure out exactly
> what frame it is failing on and then setting "startframe" and "endframe"
> to analyze *just* that frame and see if you can reproduce the error. I
> have never seen this behavior before, so I'm not quite sure what else to
> try at this point.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Pin-Chih Su (Henry Su)
Ph.D.
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office 312-996-5388
fax 312-413-9303
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Received on Tue Aug 04 2015 - 11:00:02 PDT
