I wish to find all protons that come within a certain
distancd (say 3 angstroms) from a specified atom (another
proton) during a md run.
You could use DISTRIBUTION DIST with solute being the specified
atom and solute being the others, dump the raw distances, and
filter this file according to your criteria, e.g. using awk or
perl. It may require modifying carnal to print a list of
which columns in the table map to which pairs. Alternatiely,
all the likely pairs could be specified in explicit distance
measurements.
I tried to use cutres in carnal but it seems that option
will only give me residues as in monomers
Cutres is intended for generating lists of residues for belly
runs in sander.
Bill Ross
Received on Sat Oct 13 2001 - 12:50:04 PDT
