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? James 2014-04-30 1:43 GMT+04:00 Elaine Meng <meng@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....
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....
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@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