[phenixbb] phenix.geometry_minimization with amber option

Nigel Moriarty nwmoriarty at lbl.gov
Thu Mar 12 10:47:49 PDT 2020


Wei

This is currently broken but I'm working on it.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Wed, Mar 11, 2020 at 9:03 AM Wei Wang <ww2283 at columbia.edu> wrote:

> Dear all,
>
> I try to use phenix.geometry_minimization with amber option, but when
> reaching minimization step, the function always crash. If I don’t use amber
> option, then it’s ok.
>
> The commands I put in was like:
>
> phenix.geometry_minimization 4phenix_xyz.pdb amber.use_amber=true
> amber.topology_file_name=4amber_xyz.prmtop
> amber.coordinate_file_name=4amber_xyz.rst7
> amber.order_file_name=4amber_xyz.order
>
> I tried both 1.17 stable and latest overnight build. Please share your
> advice, thx!
> Wei
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20200312/018a2b86/attachment.htm>


More information about the phenixbb mailing list