Re: [AMBER] Order of the atom in prep ourput of antechamber

From: Hannes Loeffler <>
Date: Fri, 10 Jul 2015 10:01:52 +0100

On Fri, 10 Jul 2015 10:52:24 +0200
Nicholus Bhattacharjee <> wrote:

> Hello all,
> I am trying to prepare prep file with antechamber using mol2 file
> which include the charges. However I find that antechamber changes
> the order of the atoms from that present in the mol2 file. Is it
> inherent property of antechamber or is there any other key word in
> the command which keeps the order of the atom.
> my command is as below
> $ antechamber -i Mol-ia3_m1-c1.mol2 -fi mol2 -o pep.prep -fo prepi
> I am including the initial mol2 and final prep file as attachment.
> Thanks in advance for suggestion.

The prepi format uses internal coordinates and so antechamber needs to
find a suitable starting point and then follows the molecular bonded
network. While there may be multiple options how to solve this it
mostly likely will lead to a different atom order than in the original.

Is there a particular reason why you need a prepi file an cannot just
use the original mol2 format?


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Received on Fri Jul 10 2015 - 02:30:02 PDT
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