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

James Starlight jmsstarlight at gmail.com
Wed Apr 30 03:21:05 PDT 2014

Hi Elaine,

thanks for suggestions. Could you tell me if it's possible to use some
scripts to make system preparations using amber parameters without
Chimera's GUI?


2014-04-30 1:43 GMT+04:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> ----------
> 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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