The same happens to me once and, looking closely to the trayectorie files, in one frame there was an error and the ligand goes 100 A away from the complex, so I repeated the simulation and the problem was solved. Maybe is that type of error
________________________________
De: Kankana Bhattacharjee via AMBER <amber.ambermd.org>
Enviado: jueves, 7 de septiembre de 2023 10:38
Para: AMBER Mailing List <amber.ambermd.org>
Asunto: [AMBER] MMPBSA issue:
Dear AMBER users,
I have performed protein-ligand binding affinity using MMPBSA using amber
22 version. I did the analysis for the 200 and 2000 frames from the last 20
ns. I am trying to reproduce one paper's result. In case of 200 frames
contribution matched closely with reference result but, while using 2000
frames, standard deviation is found to be extremely high (~+-50-100) !!
Also, free energy of binding is found to be comparatively higher than the
actual result.Single trajectory approach is used and one complex trajectory
is used for the MMPBSA analysis.
Kindly suggest me regatrding the issue. Should multiple complex simulations
have to be performed ?
Thanks & Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Mon Sep 11 2023 - 01:00:02 PDT
