AMBER: Bug and Patch in ANAL

From: Andy Purkiss <>
Date: Wed, 04 Aug 2004 16:38:30 +0100

Dear all,

Whilst trying to undertake energy decomposition of the interaction of
two peptides, I've located a bug in anal.

Example 3 in Appendix B, GROUP specification was not working correctly,
instead of splitting the input residues into one group per residue, I
was getting 0 atoms selected and an error: ***PROBLEMS WITH GROUPRES

I have traced this to the file amber7/src/lib/rgroup.f. Line 167 appears
to be the culprit. The original reads:
          IF(ITIME.EQ.2.AND.IGRP(1).LT.0) LSIGN = 1
patching this to
          IF(ITIME.EQ.1.AND.IGRP(1).LT.0) LSIGN = 1
gives the correct splitting of the group into separate residues.

I understand that anal is no longer documented, but I thought this might
be of interest, as there is currently no alternative that I know of for
quick and dirty energy decomposition.

Andy Purkiss

      "I have not failed 10,000 times. I have successfully 
      found 10,000 ways that will not work" (Thomas Edison)
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 04 2004 - 16:53:00 PDT
Custom Search