Hello Dr. Roe,
Actually I answered my own question with the atominfo .H* command, which
printed out all the necessary information about the hydrogen atoms I was
analyzing. Is there a way to save the output of these info commands to a
dataset short of copy-pasting from the terminal/logfile? I would love to
automatically save it as a CSV or tab-delimited file.
Thank you,
Eugene Yedvabny
On Sun, Jun 29, 2014 at 9:44 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>
wrote:
> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org <javascript:;>
>> > 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)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Jun 29 2014 - 22:00:02 PDT
