AMBER Archive (2005)

Subject: AMBER: reordering atoms after antechamber

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 25 2005 - 11:02:38 CST


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_at_eml-r.villa-bosch.de <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de> Additional info: my home page <http://projects.villa-bosch.de/mcm/people/cojocaru/>

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