Re: AMBER: A script file for measuring the distance between 2 atoms during MD

From: Thomas Cheatham <>
Date: Wed, 27 Sep 2006 12:05:25 -0600 (Mountain Daylight Time)

> I have the following script to measure the distance of
> the 67.OD1 and 110.NZ in a protein during MD. However
> when I run using $AMBERHOME/exe/ptraj *.prmtop <
>, it takes very long time and never ends
> for almost 1 hour thus I doubt there is something
> wrong. Will you please take a look and see what is
> wrong?
> ------------------------------
> trajin complex_md1.mdcrd
> distance DIST 67.OD1 110.NZ out 926MD1_distance.out
> strip :WAT
> go

ptraj prints out a lot of status information, and without this I cannot
determine what is going on. Also, you do not have the correct format for
the mask strings which should be :67.OD1 :110.NZ. I also do not see why
you need to strip the :WAT residues as this is irrelevent (since you are
not outputing a new trajectory or doing anything after the strip). I
highly recommend, *again*, to go through the tutorials...

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Received on Sun Oct 01 2006 - 06:07:06 PDT
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