Re: amber-developers: Amber/APBS module outline

From: David A. Case <>
Date: Wed, 12 Apr 2006 08:46:53 -0700

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
> and
> 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
Received on Fri Apr 14 2006 - 03:25:44 PDT
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