Re: [AMBER] Errors with .dcd files using MMPBSA

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Wed, 6 Sep 2023 09:49:59 -0700

Make sure you converted the files correctly. You can check the
consistency between your mdcrd and prmtop by visualizing them in VMD
first.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Sep 6, 2023 at 1:31 AM VERONICA MARTIN HERNANDEZ via AMBER
<amber.ambermd.org> wrote:
>
> I'm running a MMPBSA calculation but when I convert the .dcd files to .mdcrd with cpptraj and the ejecute the MMPBSA.py module, In the final results I get the following error:
>
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
> TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
>
> How can I solve thsi problem without runnig the simulation again?
>
> Thanks in advance
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I5JYxoes6LH2f_E3-D-q_EuDyTzTynK_GTm5fknvI4M670x47usx10VGBS1bHD73yXt9Ts930_U7Mw$
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 06 2023 - 10:00:02 PDT
Custom Search