AMBER Archive (2008)

Subject: AMBER: distance

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Fri May 09 2008 - 09:36:18 CDT

Dear Amber users,

I tried to calculate the distance between two atoms but I am
getting the following error.

PTRAJ: distance DIST :4760_at_O:2126_at_HE2 out DIST.list
Mask [:4760_at_O:2126_at_HE2] represents 1 atoms
WARNING in ptraj(), distance: Error in specification of the second mask
Ignoring command
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 1250 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (PROD1.mdcrd) is an AMBER trajectory (with box info) with 1250 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

NO ACTIONS WERE SPECIFIED

The input command what I have given is :

trajin PROD1.mdcrd
distance DIST :4760_at_O:2126_at_HE2 out DIST.list

I cant understand what is going on. Could someone tell me what is wrong with my command?

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg
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