[Chimera-users] Chimera MD: minimization not adding Hs

[Elaine Meng]

Hi Laura,
You would need to use menu: Help... Report a Bug and attach the specific structure or a session file, so we could try to reproduce the problem.  If we can't reproduce it, it is unlikely we could do anything about it!   Also it would be great if you did that when you got the error, because then the report would include the error.  There is a "Report Bug" button on the bottom of the error window that opens the same reporter dialog as from the Help menu.

I tried a small peptide and didn't have the problem.  When I clicked the Run button on Molecular Dynamics Simulation, the Dock Prep tool appeared, hydrogens were added, charges assigned, etc. as normal and minimization was successful.  Minimization needs hydrogens and charges, so it does not make sense for minimization to work and then equilibration to fail, unless the reason for the equilibration problem was something else (not  because of missing hydrogens and charges).

In the bug report please describe what you did and what happened, attach data (the peptide structure or a session file allowing the error to be reproduced), and include your e-mail address if you want feedback.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 1, 2020, at 8:20 AM, Laura Juszczak <LJuzak at brooklyn.cuny.edu> wrote:
> 
> Dear help:
> In running an MD on an aromatic dipeptide from Chimera installed on my Mac, the minimization step within the Run Parameters does not add required Hs even though that option is checked, resulting in a n equilibration error message re missing Hs. However, if I choose to minimize outside of MD simulation (Tools—> structure editing—> minimize structure), Hs are successfully added, and are visible on the model. Returning to MD simulation, I am able to proceed to equilibration and production successfully.
> Laura J