[Chimera-users] Preparation of the protein-ligand system for the amber simulation

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 29 14:43:51 PDT 2014


Hi James,
I believe not - one of the main limitations is that there is very little ability to use anything other than the parameters you get from the force field choices listed in the dialog for standard residues and the Antechamber process automatically used for nonstandard residues (i.e. small molecules).  You can only substitute in different partial charges for nonstandard residues, and even that is rather  labor-intensive:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>

Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 29, 2014, at 3:45 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera Users,
> I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example
> Thanks for help,
> James




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