Re: [AMBER] Printing out matrix labels

From: Daniel Roe <>
Date: Fri, 27 Jun 2014 22:13:10 -0600


The command 'select .H*' or running cpptraj like:

cpptraj -p <topology> --mask '.H='

will print the resulting selected atoms in a parseable format.
Unfortunately there isn't currently a way to label matrix output directly
yet, but that is a good idea.


On Friday, June 27, 2014, Eugene Yedvabny <> wrote:

> Hello Amber community,
> I am using the cpptraj command *matrix dist .H* *to generate a distance
> matrix between all the hydrogen atoms in my protein (this is run after
> stripping the solvent). Is it possible to print out the labels for the
> matrix so I know which hydrogens correspond to which row/column? I assume
> that the .H* mask just loops through all H atoms, so if printing the matrix
> labels is not possible, is there a command that will print out just a list
> of Residue-Atom for all matched hydrogens, akin to the labels used in hbond
> command?
> Thank you,
> Eugene Yedvabny
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> AMBER mailing list
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jun 27 2014 - 21:30:02 PDT
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