Hi AMBER
I am attempting to track a specific water as it migrates through the
protein by measuring its distance from a key residue. However, the
problem is that although the topology file seems to number ALL the
waters the pdb files made from it using "ambpdb" or ptraj seems to have
problems when there are a large number of water molecules. I get WAT
residues with ****** as the residue or ****** as the atom number. Thus,
I cannot coordinate the WAT residue from the pdb file to the
trajectory/prmtop files.
Has anyone solved this problem? Am I missing something?
Thanks, Steve
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Received on Sun May 04 2008 - 06:07:27 PDT
