Hi,
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,
Th.
Gesendet: Freitag, 10. Juli 2015 um 11:01 Uhr
Von: "Hannes Loeffler" <Hannes.Loeffler.stfc.ac.uk>
An: amber.ambermd.org
Betreff: Re: [AMBER] Order of the atom in prep ourput of antechamber
On Fri, 10 Jul 2015 10:52:24 +0200
Nicholus Bhattacharjee <nicholusbhattacharjee.gmail.com> 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?
Cheers,
Hannes.
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Received on Fri Jul 10 2015 - 03:00:03 PDT
