VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Aug 19 2020 - 10:04:21 CDT

Haha - I stand corrected! Sorry for overgeneralizing from my own experience.

Best,
JC

> On Aug 19, 2020, at 8:32 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> Hi JC, many of my coworkers are still using an old build of Dowser.
>
> To recall for the list, this code has not been available publicly since the developing PI retired and the (taxpayer-funded) software is not available for download any more.
>
> I have looked at the proposed successor: http://stuchebrukhov.ucdavis.edu/dowserplusplus/ <http://stuchebrukhov.ucdavis.edu/dowserplusplus/> but it was far from being functional on the same input PDB files that the old Dowser could easily deal with. Looking closer at a few of the citations of the Dowser++ paper, I saw a mixture of:
> - papers introducing other water-placement methods, and citing it for context;
> - review articles;
> - a few application papers that cite it as a reference for the old Dowser.
> I have not seen yet a paper that discussed the use of "Dowser++" in the methods. Did anyone?
>
> Giacomo
>
> On Wed, Aug 19, 2020 at 8:04 AM JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> You can safely skip it. I don’t think anyone uses Dowser anymore.
>
> Best,
> JC
>
>> On Aug 18, 2020, at 1:14 PM, Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu <mailto:hmnasrullah.faisal_at_ndsu.edu>> wrote:
>>
>> Hi all,
>>
>> I am looking for a tutorial of Dowser for membrane protein modeling. The links given in https://www.ks.uiuc.edu/Research/vmd/plugins/dowser/ <https://www.ks.uiuc.edu/Research/vmd/plugins/dowser/> are not working.
>>
>> Thanks
>> Faisal
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>