AMBER Archive (2002)

Subject: antechamber created prep file--Problem in xleap--additional info

From: Sarangan Ravichandran (sravi_at_ncifcrf.gov)
Date: Tue Jul 16 2002 - 09:06:31 CDT

 
Hi All:

I have trouble in reading prep
file (created by antechamber) into
xleap. xleap exits with the following
message

-----------------------------------------------------
 !FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found
!
!ABORTING.

----------------------------------

The leap.log has the following message

 Bond: Maximum coordination exceeded on .R<AMB 1>.A<H1 4>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<AMB 1>.A<C4 5> .R<AMB 1>.A<H1 4>

Thanks

Ravi