Re: [AMBER] Atom name convention/conversion in antechamber

From: <>
Date: Tue, 29 Mar 2011 08:45:09 +0200

Hi Dave,

this may be a stupid question, but what file format would you recommend to
define a new residue for leap?
What Ive done up to now is the sequence
antechamber -> prepin file -> leap -> *.{crd,top}

Does leap read ac files which someone else recommended? I haven't found
anything in the documentation nor the code...

And as I do softcore TI calculations where the ordering of the atoms in the
input files is crucial I thought that only the prepin file with the tree info
can really ensure the order that I need (if I have larger changes, it
occasionally happens that molecular tree is different in the two prepin files
and I have to manually resort and "re-tree" there a recommended,
more intelligent and less tedious way to do this??).

BTW, what are the other issues about prepin files I should be aware of?


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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-----Ursprüngliche Nachricht-----
Von: case []
Gesendet: Sonntag, 27. März 2011 01:33
An: AMBER Mailing List
Cc: Junmei Wang
Betreff: Re: [AMBER] Atom name convention/conversion in antechamber

On Thu, Mar 24, 2011, wrote:
> here is a simple example, methylene chloride:
> The pdb file is:
> HETATM 1 C * 0 0.000 0.000 0.000 1.00 0.00 C
> HETATM 2 CL * 0 1.773 0.000 0.000 1.00 0.00 CL
> HETATM 3 H2 * 0 -0.363 0.727 0.727 1.00 0.00 H
> HETATM 4 H3 * 0 -0.363 -0.993 0.266 1.00 0.00 H
> HETATM 5 H4 * 0 -0.363 0.266 -0.993 1.00 0.00 H
> CONECT 1 3 4 5 2
> CONECT 2 1
> CONECT 3 1
> CONECT 4 1
> CONECT 5 1
> The antechamber command:
> antechamber -i test.pdb -fi pdb -o test.prepin -fo prepi
> As you can see, the IGRAPH in the prepin file for the chloride has been
> changed from CL -> Cl.

I can confirm that the current developer's code still has this problem. The
problem goes away if the output format is mol2. (Another reason, among many,
to avoid the prepi input if possible.)

I'm cc-ing this to Junmei to see if he has any ideas.

...thanks for the report...dave

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Received on Tue Mar 29 2011 - 00:00:05 PDT
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