AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
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,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | 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 amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu