Re: AMBER: using packmol file in Amber

From: David A. Case <>
Date: Thu, 4 Dec 2008 11:32:49 -0500

On Thu, Dec 04, 2008, oguz gurbulak wrote:

> I created a lib file and loaded it into leap . And also I generated a
> packmol pdb file and added TER cards into the packmol pdb file. But after
> I load packmol pdb file to leap , same errors and warnings happened. I
> attached the packmol pdb file. Could you please help me about this problem?

This is really quite frustating to people reading this list, who would like
to help you. Here is what is missing:

1. You describe in pretty vague terms what you did ("created a lib file",
"loaded it into leap", etc). But you don't say *exactly* what you did, and
that is crucial.

2. You say you got the "same errors and warnings", but as far as I can tell,
you never really posted those. In any event, you should re-post: most people
don't have the time to search back through the archives to find some old error
messages. Plus, your previous posts referred to a residue named "HEP", but the
current pdb file just has residues named "OAS". So, it's hard to believe you
acutally got the "same" error messages.

3. Here's was my suggestion from before:

> Suggestion: start small, and work one step at a time. Be sure that you can
> read and process a single HEP structure.

There's no indication that you tried that. If you can't load a single
molecule, you probably can't load multiple molecules.

Without knowing how you created the lib (and frcmod?) files, and without
knowing what the error messages are, no one will be able to help.

Sorry to come down hard on you, but problem reports need to be specific and

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Received on Fri Dec 05 2008 - 18:44:26 PST
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