Date: Tue, 10 Aug 2010 10:51:53 -0500
I am running unfolding simulations on an 81-redisue protein in explicit water (ca. 7500 water molecules). I want to determine the closest 100 water molecules to the protein during and at the end of the simulation. My ptraj script is as follows:
#!/bin/csh
ptraj file1.prmtop << EOF
trajin file2.nc
solvent byres :WAT
closest 100 :1-81 first
average near100.pdb pdb
EOF
The pdb file that is created when I run this script shows only water molecules clustered within the nucleotide binding site of the protein. There are no water molecules anywhere else around or within the molecule. Yet, the starting x-ray structure shows that water molecules are distributed evenly around the protein. Is there something wrong with my ptraj script? Should I be doing something else?
John
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