This error is because the script is unable to find the ptraj module. You
must have $AMBERHOME set (i.e. export AMBERHOME=/usr/local/amber10/) and
have $AMBERHOME/bin in your path for MMPBSA.py to work properly.
Furthermore, make sure that AmberTools has been compiled properly and ptraj
is in $AMBERHOME/bin.
Good luck!
-Bill Miller
On Thu, Feb 25, 2010 at 10:02 AM, Aurum Bai <javacfish.yahoo.com.cn> wrote:
> Dear all,
>
> I repeat to do "Nmode calculation" for ras-raf.(
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm).
> But I face the problem:
>
> when I run "$AMBERHOME/exe/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp
> ras.prmtop -lp raf.prmtop -y *.mdcrd",
>
> then the err shows:
>
> "Error: ptraj is needed for MMPBSA
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files."
>
> But I have parpare all the file (contain *.mdcrd) for the Nmode
> calculation.
>
> what is wrong with it? How do i solve it ?
>
> javacfish
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 25 2010 - 08:00:03 PST
