Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points

From: Ray Luo <rluo.uci.edu>
Date: Mon, 31 Jan 2022 10:59:52 -0800

Hi Shiyu,

If you have some sample files with a few (i.e. three to five) snapshots for
me to recreate the issue, that would be great. Please email me off the list.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Mon, Jan 31, 2022 at 10:26 AM David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Jan 19, 2022, 王世玉 wrote:
> >
> >1. whether we also could compute MMPB(GB)SA after add Extra Points in
> Amber
> >Topology File?
>
> There have been reports of odd behavior from MMPBSA using extra points,
> but I
> don't know that these were ever duplicated or resolved.  Maybe Ray or
> others
> have a better memory than I do.
>
> >
> >2. where could I download the amber version that could simulate Extra
> Points？
>
> All versions of Amber support extra points.  If you find problems, please
> let us
> know.
>
> .....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 31 2022 - 11:30:02 PST
Custom Search