Dear David,
I have a total of 2000 frames in the trajectory.
How many would you consider sufficient for this type of complex with a
total of 234 residues?
I tried the nmode calculation with 2 frames but it did not print the final
results and exited without any error message.
I will try to reproduce that, check for any printed error messages and post
them here soon for further advice.
Thanks a lot for useful comments and suggestions.
Best regards.
Vaibhav
On Mon, Apr 19, 2021 at 6:48 PM David A Case <david.case.rutgers.edu> wrote:
> On Sun, Apr 18, 2021, Vaibhav Dixit wrote:
>
> >I'm getting very high entropy values after running the MMPBSA with the
> >following input.
>
> Quasi-harmonic entropies are very difficult to converge. I would think
> that
> using only 400 frames is way too few. Have you tried doing the entropy
> calculation (only) with many more frames? [You don't need the MMPBSA.py
> program here--just use cpptraj.]
>
> Also, try using the normal mode model (you generally would not need very
> many frames here, but you can check to see what the difference is from one
> frame to the next.) When things are working and converged, the two
> estimates should not vary by a lot. If you have a weak binding affinity,
> you are facing a problem that may require a lot of careful attention to get
> reliable answers.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 19 2021 - 07:30:03 PDT
