I'll give it a shot this weekend.
Best,
Ray
David A. Case wrote:
>On Tue, Apr 11, 2006, Robert Konecny wrote:
>
>
>>I have written Amber/sander interface to APBS which allows access to most
>>of the APBS functionality from within sander.
>>
>>
>
>
>
>>Documentation
>>for the current, beta version of the Amber/APBS module is available at
>>http://morgan.ucsd.edu/iapbs/ and
>>http://morgan.ucsd.edu/iapbs/usersguide/index.html The code can be also
>>donwloaded from there together with Amber9 patches.
>>
>>So after this long introduction (sorry), I'd like to ask if the outlined
>>Amber/APBS implementation makes sense. I'm not an Amber expert so although
>>the current module seems to work fine (in my limited testing) it is
>>certainly possible I may have overlooked something. One obvious thing is
>>that the current use of igb=6 is not very clean and it can be probably
>>confusing for the users. So I'd welcome any comments, recommendations or
>>ideas you might have.
>>
>>
>>
>
>Hi Robert:
>
>This all looks very nice! It will probably take people here a little time
>to actually try it out, so you might have to wait a bit for real feedback.
>Ray Luo is probably the best person to comment, since he wrote the PBSA
>module now in sander.
>
>To me, it looks like there are two main things this provides:
>
>1. The ability to directly and easily compare pbsa and APBS results, in terms
>of results, dependence on grid spacing, computational efficiency, memory use,
>and so on.
>
>2. This comparison might be especially interesting for the "pure implicit
>solvent dynamics", since this is a new feature for sander/pbsa, and yet is one
>that people have a lot of interest in pursuing.
>
>A couple of comments:
>
>1. Unlike Amber 8, in Amber 9 the "igb=6" option is no longer unused, but
>is rather used for the case of no dielectric boundary. So, I suggest that you
>turn on iAPBS with igb=11 instead. This has the advantage of being adjacent
>to igb=10, which is the analogous switch for pbsa.
>
>2. If it looks promising, we should incorporate this into the Amber 10 CVS
>tree, so that developers will get it automatically. This will greatly reduce
>the activation barrier for having people try it out. For now, however, we'll
>try the method you have on the web page, above.
>
>...thanks again....dave case
>
>.
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
http://www.rosswalker.co.uk/movie_sounds/
Received on Fri Apr 14 2006 - 03:25:44 PDT
