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 |
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Received on Sat Apr 09 2011 - 22:30:03 PDT
