AMBER Archive (2008)

Subject: RE: AMBER: Newbie question: partial minimization in implicit solvent

From: Ross Walker (
Date: Wed Nov 12 2008 - 15:00:39 CST

Hi Jochen,

> However, the manual says (Amber9/10) that GB implicit solvent minimization
> using constraint atoms is currently not possible. On the other hand,
> DOCK6.1
> apparently allows the definition of frozen atoms upon GB minimization
> in the context of amber_score. Is there a workaround for doing this in
> native Amber?

This is a limitation of sander's gb implementation. NAB supports it which is
what I believe the Dock implementation is based on. I wrote a version of
egb.f for sander v9 a long time ago that fixes this limitation. A patch is
attached which you can apply to amber 9 with:

mv sander9_gb_belly.patch $AMBERHOME/src/sander
cd $AMBERHOME/src/sander
patch -p0 <sander9_gb_belly.patch

This only works against amber 9 (I haven't had a chance to do it for Amber
10). I also have only tested it again the released version (so it is
possible that some of the bugfixes could mess up the patch but you should
get a message about patching failed if that is the case).

Feel free to try this but please use it at your own risk, I haven't
extensively tested it to make sure it is strictly correct, I just 'think' it

The alternative would be to do the minimization in NAB instead of sander.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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