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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
848-445-5239
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 28 2012 - 13:00:02 PST
