AMBER Archive (2008)

Subject: Re: AMBER: distance

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Fri May 09 2008 - 09:49:37 CDT

Hi,

  I'm not sure if it is a typo in the email or not. But the mask selection
should be:

  distance Dist :4760_at_O (space) :2126_at_HE2 out DIST.list

  HTH,
 Ibrahim

On 5/9/08 10:36 AM, "Urszula Uciechowska"
<urszula.uciechowska_at_pharmazie.uni-halle.de> 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
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