you are missing a space :)
distance DIST :4760.O :2126.HE2 out DIST.list
or the name of your atoms is not right,
use
ambmask -p PRMTOP -c PRMCRD -find '(:4760,2126)'
to see the definition of your residues
Good luck!
EM
Urszula Uciechowska wrote:
> Dear Amber users,
>
> I tried to calculate the distance between two atoms but I am
> getting the following error.
>
> PTRAJ: distance DIST :4760.O:2126.HE2 out DIST.list
> Mask [:4760.O:2126.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.O:2126.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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Received on Sun May 11 2008 - 06:07:44 PDT
