AMBER Archive (2008)

Subject: RE: AMBER: ptraj problem with imaging

From: fatima.chami_at_durham.ac.uk
Date: Thu Jul 03 2008 - 11:11:19 CDT

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

>
> Hi Fatima,
>
> Are you certain you gave ptraj the correct prmtop file? That is a periodic
> prmtop file?

I thought but the name of the prmtop was misleading.. i had to use rdparm to
strip water and use it for my MD solute trajectory only. Now it is working.
Many thanks

Another thing is imaging implicit for time correlation analysis in ptraj

best wishes
Fatima

>
> 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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> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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