[Chimera-users] Molecular Dynamics

[Elaine Meng]

Hi Edmund,
Yes and probably yes, but you would have to try to use it on your specific system to see -- the main sticking point is whether the automated tools in Chimera for parametrizing the atoms can handle the system, e.g. whether it has unusual bonds, nonstandard residues, unsupported metal ions, etc.

The bigger picture, however, is that Chimera minimization and dynamics are meant to be user-friendly and convenient, but they are relatively slow (calculation not optimized for speed) and cannot handle all situations, and do not have many options that are provided by dedicated molecular mechanics/dynamics packages such as AMBER, CHARMM, GROMOS, GROMACS, etc.  If you want to do very long simulations or get ANY quantitative results, you should use one of those other packages.  Then you can view/analyze the trajectory output from them in Chimera if you want.

It sounds like your system and especially peptide ligand may be highly flexible and might require a longer simulation, depending on what you are trying to get from the calculation.

All the documentation we have for the Molecular Dynamics tool is in its help page, what you get by clicking the Help button or by viewing the copy at our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

The tool uses MMTK and adjusts some options of that program, so this help page simply repeats or links to MMTK documentation, since that was all the information I had.  The tool was developed in collaboration with the Marechal group in Barcelona.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 17, 2020, at 7:11 PM, Edmund Marinelli <edmundmarinelli at gmail.com> wrote:
> 
> Hello:  
> 
> Very new to Chimera and to modeling in general.  
> 
> 1.) Does the Molecular Dynamics Tool allow simulation of a protein ligand complex?
> 
> 2.) Does a protein ligand docking pose generated by Autodock, for example, qualify as a 'model' that can be read by the MD Tool and be employed in a MD run? 
> 
> Is there a comprehensive tutorial or manual discussing in detail the setting of MD run within Chimera?  
> 
> Any help would be appreciated. Thanks.
> 
> Edmund R Marinelli, PhD