AMBER Archive (2008)

Subject: RE: AMBER: ptraj problem with imaging

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 02 2008 - 15:06:42 CDT

Hi Fatima,

Are you certain you gave ptraj the correct prmtop file? That is a periodic
prmtop file?

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of fatima.chami_at_durham.ac.uk
> Sent: Wednesday, July 02, 2008 9:53 AM
> To: amber_at_scripps.edu
> Cc: ross_at_rosswalker.co.uk
> Subject: AMBER: ptraj problem with imaging
>
> Dear Folks,
>
> Ptraj does not seem to image my MD trajectory which run for 25ns.
> Despite this message :
>
> ACTIONS
> 1> IMAGE by molecule to box center using the first atom, atom
> selection *
> (All atoms are selected)
>
> but no imaging ..i tailed the last lines of each mdcrd noimaged and imaged
> and
> they look the same a part from that ptraj stripped the box information in
> the
> trajout file
> --------------------------------------
> trajin run.mdcrd
> image center
> trajout run_img.mdcrd trajectory
> ---------------------------------------
>
> % tail run.mdcrd
> 280.389 139.553 -75.674 110.504-125.782 -22.627 295.316 191.568 -43.216
> 106.793
> -214.410-102.750 238.944 -50.918 214.620 188.840
> 48.163 47.513 47.889
>
> % tail run_img.mdcrd
> 280.389 139.553 -75.674 110.504-125.782 -22.627 295.316 191.568 -43.216
> 106.793
> -214.410-102.750 238.944 -50.918 214.620 188.840
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