Hi,
there are many programmes which study the protonation states of
amino acids and then modify them according to their state.
One of the programmes is propoka:
http://propka.ki.ku.dk/
Hope this helps,
Lamees
On Thu Aug 19 12:45:33 EDT 2010, George Tzotzos <gtzotzos.me.com>
wrote:
>
> 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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>
--
Hegazy,Lamees
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Received on Thu Aug 19 2010 - 10:00:08 PDT
