AMBER Archive (2008)

Subject: Re: AMBER: distance

From: E.M. (pckboy_at_gmail.com)
Date: Fri May 09 2008 - 09:43:12 CDT

you are missing a space :)

distance DIST :4760_at_O :2126_at_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_at_O:2126_at_HE2 out DIST.list
> Mask [:4760_at_O:2126_at_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_at_O:2126_at_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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu