I guess you are trying to see the first hydration shell around it. If so,
you'd better to check it with the RDF function of water around it.
The ptraj input is quite easy, and if you just change the name of the files,
you can get it.
trajin file.mdcrd
radial rdf_output 0.05 10.0 :Solvent_mask :Solute_mask
go
Then you analyze the thickness of the 1st hydration shell, select it using
VMD, for example, with the following command:
Go to Graphics --> representation
Select atoms and type:
*water and within your_thickness of your_disscharide*
Then you just need to count how many waters are left, or generate a new pdb
with this structure.
This the approach I'm currently following, but of course there are thousands
of different ones.
You can also directly use the *watershell* command on ptraj.....
On Thu, Jul 28, 2011 at 6:51 AM, subrata paul <paul.subrata34.gmail.com>wrote:
> I want to calculate number of water molecule around a disscharide(25
> disscharide).
> to caculate no of water molecule around O2
> my ptraj in file is..
> trajin NVT-md-0u20.mdcrd
> center :1-1450 origin mass
> image origin center familiar
> donor mask :1-50.O2
> acceptor WAT O H1
> acceptor WAT O H2
> hbond distance 3.5 angle 120.0 nosort series time out hb.dat
>
> Is this in put file is ok or I have to edit?
>
>
> from the result how we will count the number of molecule??
>
> thanking you
> subrata
> IIT guwahati
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>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Jul 28 2011 - 10:00:03 PDT
