it seems that you got lots of trouble with MMPBSA.
I suggest you to
- read AMBER tutorial, follow it and reproduce it.
http://ambermd.org/tutorials/advanced/tutorial3/py_script/
- Did your amber version pass the tests?
- Per your previous emails about MMPBSA: were you issue solved? If not,
have you tried to follow corresponding instruction?
- more specific: what does 'crash' mean? What is exact error message?
Hai
On Mon, Jul 11, 2016 at 4:31 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> I am trying to do mmpbsa calculation using following script
>
>
> set amber = $AMBERHOME/bin/MMPBSA.py.MPI
>
> #Write input below
> cat > mmpbsa.in << EOF
> Input file for running PB
> &general
> startframe=1, endframe=58750, interval=2,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
>
> #Execute MMPBSA job serial version
>
> mpirun -np 16 $amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp
> PRMT7_WT_NH2.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> peptide.prmtop -y *.crd
>
> so the script crashes and there seems to be no error in the output file.
> I don't know where I am committing mistake.
> kindly help me out
>
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>
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Received on Mon Jul 11 2016 - 14:00:03 PDT
