Hello Dr. Roe,
Thank you for the tip! The select .H* command returns the list of atom
numbers, but I am looking for a more 'physical' label, i.e. "TYR_2.H" as is
used in HBond analysis. Since the select command gives me an atom index, is
there a command that prints the atom label so I can cross-reference the
two? If not, I can generate a PDB and extra the labels that way, but I
first wanted to find out if cpptraj already has this functionality built
in.
Thank you,
Eugene Yedvabny
On Fri, Jun 27, 2014 at 9:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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.
>
> -Dan
>
> On Friday, June 27, 2014, Eugene Yedvabny <eyedvabny.berkeley.edu> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
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>
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Received on Sun Jun 29 2014 - 22:00:02 PDT
