AMBER Archive (2005)

Subject: AMBER: GRID program used to add ions and solvate AMBER minimized structures

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Nov 22 2005 - 08:53:55 CST

Dear ambers,
   I would like to ask if somebody is using GRID to add ions and solvate
structures that were previously minimized in AMBER. If yes, I would like
to ask how to prepare a pdb input that is properly recognized by GRID
from amber topology and amber coordinate files ..
   I tried ambpdb with different options but GRID did not recognize
those pdb files. In fact the charge that GRID calculates is always
different than that calculated by Leap....
  
  And as a more general question: Could anyone comment on accuracy
differencies between adding ions and solvating with Leap and with GRID?

Best wishes
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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