Re: trajectory analysis

From: Bill Ross <>
Date: Sat 13 Oct 2001 12:50:04 -0700 (PDT)

        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

        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
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