[Chimera-users] Hi good morning

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 22 22:12:23 PST 2019

The Mol2 saving dialog has an option to save all models to "a single file [individual @MOLECULE sections]”

If you are preparing the structures with Dock Prep, the Mol2 saving dialog will automatically appear after the other steps are done.

The format needed for DOCK6 is described in the DOCK6 manual.  Depending on what DOCK6 options you use, you may need to edit the Mol2 file yourself after Chimera writes it, such as to add SOLVATION or AMBER_SCORE_ID for certain types of scoring, as mentioned in this page:

If you have questions specifically about DOCK6, the best place to ask is on the dock-fans mailing list:

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

> On Feb 22, 2019, at 8:16 PM, prasad ssv <prasad.ssva at gmail.com> wrote:
> How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?

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