AMBER Archive (2008)

Subject: Re: AMBER: MM-PBSA

From: Miguel Ortiz-Lombardía (ibdeno_at_gmail.com)
Date: Wed Jun 18 2008 - 09:41:12 CDT

Hi,

Attached is a very simple python script that I wrote to create symbolic
links to point to the snapshots from individual solutes (ligand, receptor,
complex) created as receptors from the three trajectories, so that they can
be used as coming from a single trajectory.

So, if your snapshots are

complex_rec.crd.###
receptor_rec.crd.###
ligand_rec.crd.###

you could use the script with:

./multilink.py complex_rec name_com complex_rec.crd.*
./multilink.py receptor_rec name_rec receptor_rec.crd.*
./multilink.py ligand_rec name_lig ligand_rec.crd.*

to get the collection of snapshots:

name_com.crd.###
name_rec.crd.###
name_lig.crd.###

which you can give to the mm_pbsa.pl script as if they would be comming from
a single trajectory. My understanding is that the standard deviations would
be correct without any further changes.

I hope it helps.

Miguel

2008/6/18 Alexander Metz <alexander_metz2000_at_yahoo.de>:

>
>
> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> --- 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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>
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