Re: [AMBER] Error while running tleap in AMBER

From: David A Case <>
Date: Thu, 15 Jan 2015 09:29:49 -0500

On Thu, Jan 15, 2015, Shreeramesh wrote:
> I ran a tleap using pdb file and I got a following error. Can you please
> suggest to solve the following error. I also attached the script for tleap
> and pbd of protein for your kind attention.
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)

This is fairly straightforward, as far as Amber messages go. Examine your PDB
file to look at the residues that are identified as having duplicate atom
names. Fix anything that needs to be fixed.

> Unknown residue: ASN number: 0 type: Terminal/beginning

Are you sure this is an error message? If you actually have problems with
the first residue, try changing its residue number. It is currently "-1".
I'd suggest trying to change that to "1" and see if that helps. I'm not
quite sure how Amber handles non-positive residue numbers, but the easy
thing is to avoid them, especially if that is really the problem.


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Received on Thu Jan 15 2015 - 07:00:03 PST
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