[AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations?

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 19 Aug 2010 09:45:33 -0700 (PDT)

I'm using tutorial 3 (http://ambermd.org/tutorials/advanced/tutorial3/section1.htm)  as a basis for conducting MM-PBSA calculations of ligands bound on small protein receptors. 

I noticed that the ras-raf.pdb file used contains hydrogen atoms.  This is not the case for the sustiva complex in the antechamber tutorial (http://ambermd.org/tutorials/basic/tutorial4b/).

My question is whether in preparing the protein complex for the MD simulation, one should first protonate the protein.

Your advice in this is much appreciated.

Best regards

George

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Received on Thu Aug 19 2010 - 10:00:06 PDT