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

From: Thomas Fox <>
Date: Fri, 10 Jul 2015 11:54:38 +0200


   if you need to preserve your input atom order for whatever reason, check out
   the MAINCHAIN functionality in prepgen (which is one of the underlying
   programs of antechamber)...I had a similar problem a while ago and I
   remember that this was the way to go. You need to write a short script to
   generate the mainchain file which defines the (as the name says) the main
   path how the atoms are connected within the molecule - thus this is a way to
   define order of the atoms in the output prepin file...then you can generate
   the prepin file with

   prepgen -i ac_file -o prepin_file -m mainchain_file

   Depending on what exaclty you need this for, you might also want to study
   the documentation for the prepin file format, I have also seen some useful
   mainchain.dat discussions in the mailing list archive.

   All the best,

   Gesendet: Freitag, 10. Juli 2015 um 11:01 Uhr
   Von: "Hannes Loeffler" <>
   Betreff: Re: [AMBER] Order of the atom in prep ourput of antechamber
   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 - 03:00:03 PDT
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