AMBER Archive (2008)

Subject: RE: AMBER: Your "bellymask-patch"

From: Ross Walker (
Date: Thu Nov 13 2008 - 12:17:58 CST

Hi Jochen,

> thank you for providing the patch! It seems to work without problems on
> the release version of Amber9. On the version that includes all recent
> bugfixes however there is some issue that i think has to do with the
> bufferlength of the "bellymask input string" in findmask.f (see last few
> sections of your patch-file). One of the bugfixes changes this length
> from 80 chars to 256. Your patch however tries to change it from an
> assumed length of 80 chars to 800 and therefore fails. I have therefore
> applied your other changes manually and left the bufferlength at 256,
> which also seems to work.

This should be fine, there was a little more to that patch file than just
the GB belly support - mainly to allow more complex belly masks to be
specified in order to support semi-flexible GB docking. However, you
probably do not need this part so the 256 is fine and you can ignore the
last part of the patch.

Good luck,

|\oss Walker

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

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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)