Re: [AMBER] Fast ibelly?

From: Ross Walker <>
Date: Tue, 20 Mar 2012 10:09:47 -0700

Hi David,

> Would it be difficult to make "belly-type" dynamics fast? I'd like to
> see whether using AMBER with a fixed protein and flexible ligand can do
> molecular docking well. (As I understand it, the current use of AMBER

It depends what you mean by 'fast'. For PME runs you still have to do the
full FFTs and you also have to do non-belly to belly atoms, so you only save
by skipping the belly-belly interactions which in the grand scheme of things
is not generally that much saving, especially considering the size of the
additional approximation you are adding. It would probably be better to look
at ways of calculating some fixed charge field and applying that to the
underlying equation but I haven't looked at it much.

> with DOCK is as a postprocessing step in which all the molecules are
> able to move, even if there are harmonic restraints, and this isn't
> faster than a normal AMBER run.)

It is a little bit faster, just not significant. It could possibly be
improved by adding logic to truly skip all belly-belly interactions, bonds,
angles etc etc. I think at the moment that is not done, the belly atom
forces are just zeroed.

> Also, why is ibelly unavailable with igb>0?

This is a tricky one. I attempted to code it a long time ago. You can apply
belly, I believe, for atoms 1 to N but not for say 100 to N. I.e. it has to
be continuous and start from 1. I attempted to add a feature to the code to
allow arbitrary choices with GB but it never really worked properly and not
enough people use Belly to make it worthwhile figuring what was wrong. I am
not sure if it was a coding issue or something more fundamental. I believe
the problem might stem from an incorrect consideration of the forces when
doing belly. There is a force due to the GB radii which are calculated
including the belly atoms. This is clearly not correct and so one needs to
figure out how to deal with this but I think the solution is non trivial.
You can't simply zero the forces since there are components there from the
GB radii which are not being 'bellied' as it were.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list
Received on Tue Mar 20 2012 - 10:30:04 PDT
Custom Search