AMBER: reordering atoms after antechamber

From: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
Date: Fri, 25 Nov 2005 18:02:38 +0100

Dear ambers,
   I used antechamber to create a prep file from a mol2 file and the
order of atoms in the output prep file was completely different than
that in the mol2 file. For some further processing I would like to have
a prep file with the same order of atoms as the initial mol2 file. Is
there any way to tell antechamber to do that?
  I also tried to load into leap the newly created prep file and then to
load a pdb file with the original order of atoms and then save a new
prep file from Leap using the coordinates of the loaded pdb file.
However, the result was the same ... Leap saved the prep file with the
order of atoms from the original prep file ignoring the order in the
loaded pdb file....

Cheers
vlad 
-- 
          Dr. Vlad Cojocaru
          EML Research gGmbH
          Molecular and Cellular Modeling Group
          Villa Bosch
          Schloss-Wolfsbrunnenweg 33
          69118 Heidelberg
          Germany
          Phone: +49-6221-533266
          Fax: +49-6221-533298
          e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
          <mailto:Vlad.Cojocaru.eml-r.villa-bosch.de>
          Additional info: my home page
          <http://projects.villa-bosch.de/mcm/people/cojocaru/>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Nov 25 2005 - 17:53:00 PST
Custom Search