Thank you very much for all of your suggestions. I really appreciate it.
Regards,
Surasak
> From: tluchko.rutgers.edu
> Date: Tue, 28 Feb 2012 13:07:52 -0500
> To: amber.ambermd.org
> Subject: Re: [AMBER] Calculate the volume of a protein from the trajectory
>
> George's suggestion is the partial molar volume and this can also be calculate with 3D-RISM directly from your trajectory. For a recent example see
>
> Awile et al. Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. PLoS Comp Biol (2010) vol. 6 (7) pp. e1000854
> http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000854
>
> You will need to strip out the solvent from your trajectory and prmtop. After this you can use rism3d.snglpnt to run 3D-RISM on every frame of your trajectory. See $AMBERHOME/AmberTools/test/nab/Run.rism_sp for an example. If you are using pure water, you can use the Xvv file from the example. If you need salt, let me know and I can provide a suitable input file.
>
> Tyler
>
> On 2012-02-28, at 9:30 AM, George M Giambasu wrote:
>
> > You can build a system that contains the same number of waters (and
> > ions) as your protein simulation, compute its average volume and
> > subtract it from the protein simulation average volume.
> >
> > g.
> >
> >>> Dear all,
> >>>
> >>> I'm wondering if there is a command in AMBER to calculate the volume of a
> >>> protein from the trajectory. Specifically, I want to calculate the average
> >>> volume of the protein from the last 10 ns trajectory. Any suggestions on
> >>> this issue would be greatly appreciated.
> >>>
> >>> Thank you very much for your help,
> >>> Surasak
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
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> ________________________________________________________________
> Tyler Luchko
> Postdoctoral Associate
> Case Group
> BioMaPS Institute
> Rutgers University
> Piscataway, New Jersey
> tluchko.rutgers.edu
> 848-445-5239
>
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Received on Wed Feb 29 2012 - 02:30:06 PST
