Hi,
My answer perhaps is out of date but I just want to add here if you or
others are interested.
You might want to play with pycpptraj, which is a python wrapper
package for cpptraj. I just made a note here based on your question.
http://nbviewer.ipython.org/github/hainm/pycpptraj/blob/master/note-books/AmberList/Matrix_label.ipynb
(if you are familiar with ipython-notebook, you will have all you need)
You can install pycpptraj by following this:
https://github.com/hainm/pycpptraj/wiki
Best
Hai
On Mon, Jun 30, 2014 at 12:51 AM, Eugene Yedvabny
<eyedvabny.berkeley.edu> wrote:
> 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 Fri Jan 30 2015 - 19:30:03 PST
