AMBER Archive (2004)

Subject: AMBER: xleap & antechamber

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue Feb 03 2004 - 03:46:54 CST

Dear all,

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
!
!ABORTING.

> 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>

Lan

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu