AMBER Archive (2002)

Subject: antechamber's prepc option

From: Matthew Lee (mrlee_at_cgl.ucsf.edu)
Date: Fri Aug 16 2002 - 14:20:59 CDT

Hi--

        Has anyone experienced any problems with antechamber's
generation of prepc files (Cartesian prep input files)? I created a
prepc file and tried reading it into tleap, but got the following
message:

ATOMS NOT BONDED: .R<*** 1>.A<H 5> .R<*** 1>.A<H 4>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found
!
!ABORTING

        I am not sure, but I think there may be a problem in the tree
specification. I no longer have acces to an old amber manual that
discusses the prep input file format, so I'm not sure, but from what I
recall, I think that antechamber is incorrectly assigning the 2nd H it
finds as an M, rather than as an E. When I changed it to an E, it
read into tleap without problems. I think this H should be an E, but
I can't recall, and the amber7 manual seems to only discuss tree names
very limitedly, in the parameter file formats, page 301. Any comments
would be appreciated.

--Matt

*******************************************************************
Matthew Randolph Lee, Ph.D.

Computational Scientist phone: (858)410-6534
Lion Bioscience Inc. fax: (858)410-6665
9880 Campus Point Drive e-mail: matthew.lee_at_lionbioscience.com
San Diego, CA 92121
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