AMBER Archive (2008)

Subject: AW: AMBER: MM-PBSA

From: Alexander Metz (alexander_metz2000_at_yahoo.de)
Date: Wed Jun 18 2008 - 05:43:18 CDT 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++

--- Neha Gandhi <n.gandhiau_at_gmail.com> schrieb am Mi, 18.6.2008:

> Von: Neha Gandhi <n.gandhiau_at_gmail.com>
> Betreff: AMBER: MM-PBSA
> An: amber_at_scripps.edu
> Datum: Mittwoch, 18. Juni 2008, 9:37
> Dear Amber users,
> 
> I am using single trajectory method for mm-pbsa analysis as
> implemented in AMber 9. In case of conformational change in
> the
> receptor and ligand, it is recommended to use 3 species
> method. i.e to
> run the MD with the ligand, receptor and complex solvated
> individually. How can I extract the final snapshots and
> energies for
> these 3 species?

You can extract snapshots from each trajectory file individually by specifying each solute (complex, receptor and ligand) as a receptor.

After doing this for all three species you can run the actual MM-PBSA calculations separately for each of the three species ... again treating each of them  as a receptor. (Alternatively you can rename the snapshots and calculate the energies for the the species alltogether ... but I think you have to to the mm_pbsa_statistics script manually anyway to get the correct standard deviations).

Then take the three *.all.out files and run the mm_pbsa_statistics.pl script manually.

gl Alexander

> 
> The other question I have is why it is recommended to use
> delphi over
> default PB-solver in Amber for charged ligands?
> 
> Many thanks!
> 
> -- 
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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