Re: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: David A. Case <>
Date: Fri, 22 Jul 2005 10:24:58 -0700

On Fri, Jul 22, 2005, Arnoult, Eric [PRDFR] wrote:
> I prepare the "prep" file for several ligands with antechamber.
> When the ligand contains an halogen atom (CL for example), the atom name for
> this halogen atom is wrote with 4 characters.
> Then, I load this "prep" file in Leap. An atom name with 4 characters seems
> to be not compatible with Leap because I obtained an error message :
> "FATAL: Atom .R<lig 276>.A<CL2> does not have type"

I can't reproduce this problem. I took a prepin file created by antechamber,
and changed one of the atom names to four characters, and everything worked
fine. There is indeed not supposed to be any restriction in Amber on four
character atom names.

I'm attaching the prepin file I tried (just edited from the one in
$AMBERHOME/test/antechamber/tp). Maybe you can try this, and can see what is
different between your prepin file and mine. If you can't figure it out,
you will have to give more details: what command led to the error? What
exactly did you do? [I just loaded my file in with loadAmberPrep, and then
used "desc" and saveAmberParm on a single ligand. You seem to have at least
276 residues.]

....good luck...dac

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Received on Fri Jul 22 2005 - 18:53:00 PDT
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