AMBER Archive (2001)

Subject: ion analysis

From: Raja Swaminathan (rajaamber6_at_rediffmail.com)
Date: Wed Dec 26 2001 - 09:56:17 CST

Dear ambers

I have done 2 ns MD on a 14 mer DNA duplex. I want to analyse the ions.

I have used the distance option in ptraj.
(i.e)I want to calculate the distance between a particular base atom for ex N6 and Na+ over the entire simulation for all the residues.

The input what i have given looks like this

distance name @Na+ 1_at_N6 test.tab noimage
distance name @Na+ 2_at_N6 test_1.tab noimage
distance name @Na+ 3_at_N6 test_2.tab noimage
distance name @Na+ 4_at_N6 test_3.tab noimage

But the output shows the nan error at some of the places and some values for some. I don't know how where i went wrong. Please give some suggestions regarding this.

Thanking you in advance

Sincerely
Raja Swaminathan