Just a thought, but you can try using VMD for that...
In the Graphics -> Representations, use something like:
"all within 5 of resid 1:81"
That will give you all the atoms present within 5 A of the PDB id's 1 to 81.
Hope it helps :)
Have a good day!
Rodrigo
-----------------------------
PhD Student
Instituto de Química
Universidad Nacional Autónoma de México
2010/12/8 Beale, John <John.Beale.stlcop.edu>
>
> I am trying to determine the 100 closest water molecules to my protein.
> This is my ptraj input file:
>
> #!/bin/csh
> ptraj file1.prmtop <<EOF
> trajin file2.nc 1 1
> center :1-81 mass origin
> image origin center familiar
> solvent byres :WAT
> closest 100 : 1-81 first
> average near100.pdb pdb
> EOF
>
> When I run the script, the pdb file shows the water molecules clustered in
> a sphere in the nucleotide binding site of the protein and not distributed
> over the entire protein. The starting x-ray structure shows that water
> molecules should be distributed around the protein and not clustered in the
> binding site.
>
> Is there something wrong with my input file (above)?
>
> Thanks!
>
> John
>
>
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Received on Wed Dec 08 2010 - 06:00:03 PST
