AMBER Archive (2007)

Subject: AMBER: distance calculation!

From: r. a. (rosajaan_at_yahoo.com)
Date: Mon Mar 05 2007 - 02:43:45 CST

Dear All
  I run 1ns simulation with 1040 frame for a protein which consists of 388 residues. so I have 1040 snapshot. For ptraj:
   
  trajin file1.crd
  distance a1 out file2.dat time 1 : 1: 388
  strip :WAT
  go
   
  I just would like to know that when we go to see the contact we need to consider the contact of residue 1 with 377 other residues, if I m not mistaken, a matrix of 388*387/2. Is there any possiblities to calculate all contact at one time. thanks for your participation.
   
  Regards
  Rose

 
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