Dear Amber Users;
I'm trying to use extract from a protein/ligand complex trajectory
intercalating waters between the ligand and the protein. There are
two sites where intercalating waters occur (at opposite ends of the
ligand) and so I'm trying to sort out how to extract these with the
"closest" command in ptraj.
Is it possible to extract waters for multiple sites using the
"closest" command? I tried using a mask that included atoms for the
first site and atoms for the second site e.g.
":protres1,:protres2:,:ligres#.ligandatom1 |
:protres3,:protres4,:ligres.ligatom10 ". This, however, does not seem
to work as it tries to get the closest water to all of these residues.
Any ideas?
Thanks
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Received on Thu Feb 04 2010 - 11:30:03 PST
