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

From: David A Case <>
Date: Sat, 11 Jul 2015 08:23:44 -0400

On Fri, Jul 10, 2015, Nicholus Bhattacharjee wrote:
> 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.

Just to augment what was said before: mol2 is generally a better output format
than prepi: many other programs can use these files, and (among other things)
the order of atoms will be preserved. The prepi format is only kept for
backwards compatibility with older scripts. New users are encouraged to
use mol2 format.


AMBER mailing list
Received on Sat Jul 11 2015 - 05:30:02 PDT
Custom Search