Re: [AMBER] Leap adds atoms to pdb (tutorial B1)

From: David A Case <>
Date: Thu, 30 Jun 2011 08:22:06 -0400

On Wed, Jun 29, 2011, Chirag Vora wrote:

> I am using AMBER 10
> Created a new atom named: H5'' within residue: .R<DT 16>

This happens because there is an atom named H5'' in your pdb file, but no
corresponding atom in the library you have loaded. The underlying problem is
that the PDB recently changed its atom names (going to version 3), and it
looks like you are seeing some problems with a new version of the tutorial and
old versions of the Amber libraries.

Probably the most straightforward thing to do is this: get the current version
of AmberTools, install it in a directory tree different from your Amber10
tree. Set your AMBERHOME variable to the new version, and use that.

You probably want to have both amber11/bin and amber10/exe in your PATH, with
the former first. That way, you will get the new AmberTools, and the amber10
version of sander, pmemd, etc.

...good luck....dac

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Received on Thu Jun 30 2011 - 05:30:06 PDT
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