Re: AMBER: PDB problems

From: David A. Case <>
Date: Fri, 15 Jun 2007 13:24:44 -0700

On Fri, Jun 15, 2007, Taryn Hartley wrote:

> Is everyone who is running simulations in Amber building their structure in
> xleap or tleap??? Is there anyone who is using a structure from the Protein
> Data Bank? and if so.... are you having problems with atom types? Is there a
> command in AMBER that automatically converts atom types? -Taryn

I would guess the vast majority of users start from files from the PDB.
"Problems with atom types" probably comes from ligands that amber doesn't
recognize -- note that most pdb files need some editing before they can be
used in Amber (or in other modeling programs).

To get any help with atom type problems, you will need to give details of
what you tried and what happened. I suspect that antechamber is the program
you are looking for, but asking for something that "automatically converts
atom types" (from what, to what?) isn't going to lead to useful replies.

[Just a guess: have you been through tutorial B4?]


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Received on Sun Jun 17 2007 - 06:07:37 PDT
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