yes i am actually want to run MMPBSA.py but it is showing this error and show no result i installed amber approx. 4 times by changing its directory but every time when i want to run MMPBSA.py it is giving different error. i download (ras-raf_top_mdcrd.tgz) this folder taking from amber advanced tutorial and paste it in amber 14 folder according to this tutorial 4 python scripts must be putted in amber 14 bin because i set amber 14 as AMBERHOME path, that 4 scripts are (MMPBSA.py, utils.py, alamdcrd.py, and inputparse.py) . But when i searched out inputparse script it was missing i could not put it into AMBERHOME/bin
after that i make an input file and i am also take it from the same site Amber Advanced tutorial that was:
and named it mmpbsa.in
Input file for running PB and GB
&general
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
and then paste it in amber 14 folder
and run the following command
$AMBERHOME/bin/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 ras-raf_top_mdcrd.mdcrd
then the terminal showing this error
InputError: Can't find input file (mmpbsa.in)
Please guide me the proper way how can i install AmberTools 14 properly and can run MMPBSA.py. its about 2 month i am stucked here and i am not successful yet please help me i want to use MMPBSA/MMGBSA in my project i am very worried i am new in Amber and ubuntu but i have to use it in my project kindly guide me step by step how can i properly install ambertools and can run MMPBSA.py i am using ubuntu 14.04 and want to install AmberTools 14. and want to run MMPBSA.py
> Date: Tue, 13 Oct 2015 07:47:53 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> On Mon, Oct 12, 2015 at 11:59 PM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
> wrote:
>
> > hi,
> > I again install amber14 and AmberTools 15 after changing directory now at
> > this time i could not find "inputparse.py" python script i don't know why
> > it is missing at this time?
> > how can i find it to place it in $AMBERHOME/bin
> > i was the following commands for installation of ambertools
> >
> > cd Downloads/amber14
> > export AMBERHOME=/home/ayesha/Downloads/amber14
> > ./configure gnu
> > source /home/ayesha/Downloads/amber14/amber.sh
> >
>
> This should set up your environment correctly.
>
>
>
> > make install
> > export LD_LIBRARY_PATH=$AMBERHOME/lib\:$LD_LIBRARY_PATH
> >
>
> Skip this command.
>
>
>
> > cd $AMBERHOME/AmberTools/src/mmpbsa_py
> >
>
> Why are you doing this? What are you doing in this directory?
>
> What is the exact error message you are getting? The Python modules for
> MMPBSA.py (namely the MMPBSA_mods python package) is no longer installed in
> $AMBERHOME/bin. But that's OK, because these files are never executed
> directly -- they are imported by MMPBSA.py.
>
> Did you actually run MMPBSA.py and get an error? What was that error?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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Received on Tue Oct 13 2015 - 13:30:04 PDT
