[AMBER] Atom name convention/conversion in antechamber

From: <thomas.fox.boehringer-ingelheim.com>
Date: Wed, 23 Mar 2011 11:47:26 +0100


when I process a pdb file with antechamber (Ambertools 1.4) to generate a
prepin file (am1bcc charges, gaff FF), I noticed that some atom names from my
pdb file are changed during this procedure. In particular, two letter halogen
(Cl, Br) names are converted from CL -> Cl and BR -> Br. This then causes
problems in leap when I try to generate the parmtop/crd files.

Now my questions:
1) Is this intended behavior, if so, why?
2) Is there a way to change this behavior - i.e. where in the code can I
change this (should I??) ?
3) Do you know of another possibility of getting my prepin files with
the "correct" == original atom names short of either manually editing the
prepin file or writing a script that automatically converts the atom names
back to the ones I need (I have tried the -a/ao name functionality, but this
didn't make any difference) ?


Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox

Boehringer Ingelheim Pharma GmbH & Co. KG
Lead Identification and Optimization Sup
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585

Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260

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Received on Wed Mar 23 2011 - 04:00:02 PDT
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