AMBER Archive (2003)

Subject: RE: AMBER: problem with file format

From: Shafinaz (shafinaz_at_bri.nrc.ca)
Date: Wed Sep 24 2003 - 15:29:10 CDT

Dear Dr. David

Thanks a lot for your mail. Following command I used for leap and the
following message I received when I try to load my pdb (molecule.pdb) file.
But leap read prep and frcmod file without any problem.

newleap -s -f /home/software_linux/amber/amber7/dat/leap/cmd/leaprc.gaff
-I: Adding /home/software_linux/amber/amber7/dat/leap/prep to search path.
-I: Adding /home/software_linux/amber/amber7/dat/leap/lib to search path.
-I: Adding /home/software_linux/amber/amber7/dat/leap/parm to search path.
-I: Adding /home/software_linux/amber/amber7/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /home/software_linux/amber/amber7/dat/leap/cmd/leaprc.gaff.
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found

I attached the pdb file and mol2 file of my compound as you suggested and
also prep and frcmod file.

Thanks a lot in advance.

With regards.

Shafinaz





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