Re: [AMBER] how to measure atom distance in md trajectories using ptraj program

From: Daniel Roe <>
Date: Wed, 28 Mar 2012 15:37:04 -0400

Ptraj and cpptraj by default use imaging when calculating distances.
If your system is periodic and you do not want to use imaging during
the distance calculation, add the 'noimage' keyword to the distance


On Wed, Mar 28, 2012 at 2:25 PM, Bala Subramani <> wrote:
> this is my input :
> distance end_to_end :6.O :7.H out  dist_end_to_endOH.list
> actually i want to measure distance between methionine carboxyl oxygen
> & aspargine n terminal hydrogen... methionine is 6th residue &
> aspargine is 7th residue in my pdb... i want to measure this
> methionine carboxyl oxygen & aspargine n terminal hydrogen distance in
> my all trajectories...totally i ve 10 trajectory files... how to do???
> i ve executed this above input & it showed the dist_end_to_endOH.list
> in dist_end_to_endOH.list, it showed me a 2 columns. column one is
> no.of frames & column two is distance values corresponding to
> frames...i ve looked into these values... shortest distance occurs in
> 32163th frame.... but wen i looked into this 32163th frame pdb in
> pymol.. the  methionine carboxyl oxygen & aspargine n terminal
> hydrogen distance varies.... could anyone tell me wat might be the
> reason for this??? thanks in advance....
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Received on Wed Mar 28 2012 - 13:00:02 PDT
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