[AMBER] Writing trajectory for C-alpha atoms

From: Ibrahim Moustafa <I.moustafa.psu.edu>
Date: Mon, 02 Aug 2010 11:31:33 -0400

Dear Users,
 
 I have an Amber trajectory (10 ns) of an entire protein structure of 400
atoms. What Iım looking for is a way to write out the coordinates for each
C-alpha along the trajectory in a single file with the same order; i.e.,
coordinates of frame1 precedes that of frame2..etc. The format of the output
file does not really matter whether it is pdb or just separate fields for X,
Y and Z. In other words, I want to have 400 files, each file has the lines
corresponding to the C-alpha coordinates through the trajectory timeline.

  I wonder if there is a way to do such analysis in Ptraj? Or any
suggestions.

 Thanks in advance for help,

 Ibrahim 

-- 
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802
Tel. (814) 863-8703
Fax (814) 865-7927
 
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 02 2010 - 09:00:05 PDT
Custom Search