On Wed, Dec 8, 2010 at 7:44 AM, Beale, John <John.Beale.stlcop.edu> wrote:
>
> 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
>
I don't know if this is a typo just in the email or not, but there should be
no space between the : and the 1. :1-81.
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 08 2010 - 06:30:04 PST
