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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