Hello,
leap will provide the necessary protons from the templates. Note that
different protonation states of various amino acids have different names.
For example, protonated aspartic acid is called ASH in amber-speak, whereas
deprotonated aspartate is called ASP. Thus, if you want leap to build a
specific residue with a specific protonation state, you have to rename all
of the residues in the PDB to match the proper protonation state in the
amber library.
A risk of keeping the hydrogen atoms in the PDB: if they do not have the
same NAME as the corresponding hydrogen atom in the library file, you will
get an error. REDUCE is a tool that can add/remove hydrogens to be
compatible with amber.
Good luck!
Jason
On Thu, Aug 19, 2010 at 12:45 PM, 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 19 2010 - 10:00:07 PDT
