RE: AMBER: problem with file format

From: Junmei Wang <>
Date: Wed, 24 Sep 2003 15:34:14 -0500

I think the reason is that the atom names in your molecule are not unique.
I guess you are using antechamber in amber7. In the new version of
antechamber , I have added the function to automatically make atom name
unique. Make sure that atom names in prep input file and pdb file are
consistent. You may consider to use this procedure: make atom names in mol2
file unique, then convert it to prep input and pdb files, then load them to


Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Homepage: Http://

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                                       RE: AMBER: problem with file format
             09/24/2003 03:29
             Please respond to

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.


(See attached file: molecule.mol2)
(See attached file: molecule.pdb)
(See attached file: molecule.prep)
(See attached file: frcmod.molecule)

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Received on Wed Sep 24 2003 - 21:53:02 PDT
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