AMBER Archive (2004)

Subject: Re: AMBER: xleap & antechamber

From: David A. Case (
Date: Thu Feb 05 2004 - 11:46:02 CST

On Tue, Feb 03, 2004, L Jin wrote:
> I used antechamber to get my prep file. But when I load the prep file into the
> xleap it always give the following error messages. Does anybody meet this kind
> of problem? Would you please anyone give me some help? Thanks a lot in advance.
> -I: Adding /usr/progs/amber/dat/leap/prep to search path.
> -I: Adding /usr/progs/amber/dat/leap/lib to search path.
> -I: Adding /usr/progs/amber/dat/leap/parm to search path.
> -I: Adding /usr/progs/amber/dat/leap/cmd to search path.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [atom.c], line 443
> !FATAL: Message: bondAtomProblem found
> !

This is a little unclear: did you get the "FATAL ERROR" message just on
staring the program, or only after the "loadAmberPrep" command described
> > loadAmberPrep "/usr/people/ljin/PROJECT2/prep/GLC/A/NS/temp.prep"
> Loading Prep file: /usr/people/ljin/PROJECT2/prep/GLC/A/NS/temp.prep
> Bond: Maximum coordination exceeded on .R<4SN 1>.A<H62 8>
> -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<4SN 1>.A<H32 9> .R<4SN 1>.A<H62 8>

You need to look at your structure around atoms 4SN, H32 and H62. You could
use an external program like Rasmol (etc.) or use xleap with the "loadPdb"
and "bondbydistance" commands. Something is wrong that is confusing

..good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to