AMBER Archive (2009)

Subject: Re: [AMBER] problem with creation of prmtop and prmcrd files

From: Tom Joseph (
Date: Wed Jun 10 2009 - 20:30:19 CDT

There is quite a bit wrong here. For example, some of your frcmod
files are screwed up and so leap did not load the extra force field
terms for your custom residues. For debugging purposes, try setting up
a much smaller system, with only one of your custom residues, and work
through the error messages from the beginning, one by one, making sure
each and every input file (prepin, frcmod, etc) is in the correct


On Mon, Jun 8, 2009 at 9:00 AM, <> wrote:
> Dear Amber Users,
> I am trying to generate the topology and coordinate files for a protein
> complexed with trna and ligand. I am getting the following error as attached in
> the file: error_file. I am also attaching the original pdb file.
> Please suggest me with a solution.
> Thanks and Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore - 560 012
> India
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> AMBER mailing list

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