Just to add on to what Ross said -- there may be an instance in which you'd
want to keep 2 different AMBERHOMEs around -- i.e. if you want to run
amber10, yet use AmberTools 1.4.
In this case, make sure that AMBERHOME points to AmberTools 1.4 (since only
AmberTools programs actually make use of AMBERHOME after installation), and
that your PATH is set up to point to AmberTools 1.4's bin directory BEFORE
it points to your amber10 bin directory.
This (and only this) setup allows you to use AmberTools 1.4 with amber <
11. Of course, you can always use an absolute path instead of ordering your
PATH variable appropriately ($AMBERHOME/bin/xleap).
Of course, if this is not the case I would strongly suggest that you get rid
of your old AMBERHOME (if not delete the files then at least get rid of all
references to it in your environment variables).
Hope this helps,
Jason
On Sat, Apr 9, 2011 at 10:20 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Zhe,
>
> > Thank you for replying immediately.
> >
> > I have already found some reasons.
> >
> > When I start xleap use "xleap" command, and
> > dna1 = loadpdb "nuc.pdb"
> > addions dna1 Na+ 0
> > it print out as my last attachment.
> >
> > But when I start xleap use "$AMBERHOME/exe/xleap -s -f
> > $AMBERHOME/dat/leap/cmd/leaprc.ff99SB"
> > dna1 = loadpdb "nuc.pdb"
> > addions dna1 Na+ 0
> > it will print out as tutorial.
> >
> > Because I contacted this software first time today, could you tell me
> > why does this difference?
> > And could you gave me some advise about studying this software?
>
> This suggests to me that there is more than one copy of xleap on your
> machine. Likely the one in your path which is run when you just type xleap
> is NOT the same one as is run when you do $AMBERHOME/bin/xleap. Running a
> different version of xleap than what your AMBERHOME points to will cause
> all
> sorts of problems.
>
> Check what xleap is in your path with:
>
> which xleap
>
> See if it matches what you expect from:
>
> echo $AMBERHOME
>
> If it doesn't then you should update your path, or best bet remove the old
> version of AMBER from your path altogether.
>
> Good luck,
>
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> 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.
>
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 09 2011 - 23:00:02 PDT
