Re: [AMBER] Distances between amino acid residues

From: Su Qiu <>
Date: Thu, 2 Dec 2010 10:46:36 +0800

Use the ptraj command. Prepare the ptraj input file as follows, (for example
if you want to calculate the distance between the N atom of residue1 and the
N atom of residue 7 in a trajctory):
this is the input file **
trajin *.mdcrd
distance end_to_end :1.N :7.N out *.list
you can name the output file as you wish.
Then type the command
ptraj *.top <
*.top refers to the top file you used for simulation.

It calculates the distance between two atoms during the simulation. You can
learn details about the ptraj command on the manual.


2010/12/1 Beale, John <>

> >From a simulation, I would like to compute the distances between amino
> acid residues that are close in space but not directly bonded. Can anyone
> tell me if they have a way to do this for all possible contacts in a protein
> molecule?
> Thanks!
> John
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Received on Wed Dec 01 2010 - 19:00:02 PST
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