AMBER Archive (2008)

Subject: Re: RE: AMBER: Tutorial B5

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Apr 23 2008 - 22:08:19 CDT

HI
Nothing changed compared the two runs.
I followed the Tutorial B5 http://amber.scripps.edu/tutorials/basic/tutorial5/index.html.

First, download the input files : prmtop, trj.5, ptraj.in.
Second, type $AMBERHOME/exe/ptraj prmtop < ptraj.in > ptraj.out

Unfortunately, I could not get the ptraj.out and any other output files, such omega 1.save...... psi 6.save etc.... in my second run.

But for my first run, I obtain all the output files.

Thanks
Lin

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Wednesday, April 23, 2008 7:24 pm
Subject: RE: AMBER: Tutorial B5
To: amber_at_scripps.edu

> Hi Lin,
>
> We need to know more information here - what do you mean by the
> commandbecame useless - what error message do you see?
>
> What is AMBERHOME set to / what is contents of $AMBERHOME/exe/ / do
> you have
> permission to run the files in this directory.
>
> What has changed since when it last worked?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> be read every day, and should not be used for urgent or sensitive
> issues.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Chih-Ying Lin
> > Sent: Wednesday, April 23, 2008 18:09
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Tutorial B5
> >
> >
> >
> > The AMBERHOME is still my environment variable.
> > But, I am still unable to use the command.
> >
> >
> >
> >
> >
> > ----- Original Message -----
> > From: Alessandro Nascimento <al.s.nascimento_at_gmail.com>
> > Date: Wednesday, April 23, 2008 5:33 pm
> > Subject: Re: AMBER: Tutorial B5
> > To: amber_at_scripps.edu
> > Cc: chihying_at_usc.edu
> >
> > > If you were able to do this before, you've most probably lost you
> > > environment variables.
> > > You can try:
> > >
> > > % echo $AMBERHOME
> > >
> > > in your shell. If it returns nothing, that's the reason. You
> can add
> > > AMBERHOME to your environment variables using
> > >
> > > % export AMBERHOME=/usr/local/amber9 (or anywhere you installed
> > > amber), if you're using bash
> > >
> > > In the manual you can see more details.
> > >
> > > HTH,
> > >
> > > --alessandro
> > >
> > >
> > >
> > > On Wed, Apr 23, 2008 at 5:13 PM, Chih-Ying Lin
> <chihying_at_usc.edu>
> > > wrote:>
> > > >
> > > >
> > > > Hi
> > > > I have been practicing the Amber tutorials B5.
> > > > And everything runs well with the following command.
> > > > $AMBERHOME/exe/ptraj prmtop < ptraj.in > ptraj.out
> > > >
> > > > http://amber.scripps.edu/tutorials/basic/tutorial5/index.html
> > > >
> > > >
> > > > But I tried to practice the Amber tutorials B5 again today.
> > > > the following command become useless.
> > > > $AMBERHOME/exe/ptraj prmtop < ptraj.in > ptraj.out
> > > >
> > > > I don't know what happened.
> > > > Should I re-install or re-compile the Amber system ?
> > > >
> > > > Thanks
> > > > Lin
> > > ----------------------------------------------------------------
> ----
> > > ---
> > > 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
> >
>
> --------------------------------------------------------------------
> ---
> 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