Date: Wed, 8 Dec 2010 06:44:42 -0600
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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