On Sep 20, 2024, at 10:05 AM, Manon Bulliard via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thank you for the quick answer. On two out of three computers we cannot find it anymore... 

The MD Simulation tool has not been removed from Chimera so there is no reason I can think of why it does not show up on those machines.  There should be 5 entries in the MD/Ensemble Analysis tools menu, the 5th of which is the MD Simulation tool.  How many entries are in that menu on those machines?

And another question, on PyMOL I have a residue called "new" and when I try to start the MD simulation it says "failure running ANTECHAMBER for residue NEW", how can I solve this issue? With a previous MD simulation that also contained a NEW residue it worked fine... 

It would completely depend on what was in residue "NEW".  If you sent me a session file with your structure I might be able to offer advice.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


Thank you in advance for your help, 

Manon

Manon Bulliard, PhD
EPFL | ISREC | Prof. Constam group
SV2837 | Station 19 | CH-1015 Lausanne

De : Elaine Meng <meng@cgl.ucsf.edu>
Envoyé : vendredi 20 septembre 2024 18:36:24
À : Manon Bulliard
Cc : chimera-users@cgl.ucsf.edu
Objet : Re: [Chimera-users] MD on Chimera
 
Hello Manon,
Nothing changed.  I just checked Chimera 1.18 right now, and it is in the same menu, Tools... MD/Ensemble Analysis... Molecular Dynamics Simulation.

Here is the help pagl, see the warning in the gray box for suitable uses of the tool:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

Regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 20, 2024, at 8:36 AM, Manon Bulliard via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
> 
> Good afternoon, 
> 
> I was using chimera to do molecular dynamic simulation. I had to download Chimera on my new computer and now have the 1.18 version. It seems this feature is not anymore present under Tools>MD/Ensemble Analysis>molecular dynamic simulation. Do you know where I can find it to still be able to perform my modeling as previously?
> 
> Thank you in advance, 
> 
> Manon

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