[chimera-dev] python script for ligand preparation

[ngayatri]

Dear Elaine,
I followed the steps to save a ligand in .mol2 file but the mol2 format file
after saving is not opening in the chimera even after adding the charges.
Please help me with what steps should i follow.

Thank You
Regards
Gayatri

On June 21, 2022 at 1:47 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Gayatri,
> There is a Dock Prep tool that does all this. Menu: Tools... Structure
> Editing... Dock Prep
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>
>
> If you mean that you have too many files to do individually with the graphical
> interface, however, you may need to figure out how do it with Chimera commands
> instead. See commands "open" to open the ligand file, "addh" to add hydrogens,
> "addcharge" to assign partial charges (and maybe other commands depending on
> what you mean by prepare) and"write" to save Mol2.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
>
> You should first try entering those individual commands in the Command Line
> one by one to figure out exactly what options you want for each ligand. After
> you know what commands and options you want to use for each ligand, then you
> can put a python script around it to loop through multiple files as described
> here
> <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 20, 2022, at 4:37 AM, ngayatri via Chimera-dev
> > <chimera-dev at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera Team,
> > I am trying to prepare separate ligand file and saving it in the .mol2 file.
> > So if you could help with script or the approach would be grateful.
> > Thank You
> > Regards
> > Gayatri
>
>
>
> For assimilation and dissemination of knowledge, visit cakes.cdac.in
>
>
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