On Tue, Oct 13, 2015 at 4:04 PM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> 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.
The first error you reported had to do with using a version of MMPBSA.py
that was released over 5 years ago, that you somehow unpacked on top of
AmberTools 15. This is not at all the recommended or documented way to
install AmberTools, and it is a way that does not work.
The remaining errors that you have posted here have all been *exactly* the
same error -- a file that you have given to MMPBSA.py on the command-line
*could not be found*. They've happened to be different files, but it is
still the same error. The file you specified did not exist. If you did
not give a full path for the file (e.g., "-i /path/to/mmpbsa.in"), then
that means that the file did not exist in the directory you executed the
MMPBSA.py command from.
The $AMBERHOME directory is ONLY the place where Amber is installed. You
should never copy tutorial files into that directory to run Amber. Ever.
This is true of every Unix program that I'm familiar with. What I do is
create a directory for a project, make sure I "cd" to that directory, and
execute all of my commands *inside that directory*. This is something you
are not doing. From what I've been able to gather from your emails, you
are downloading the tutorial files, (maybe?) extracting them somewhere,
then changing to the $AMBERHOME directory to run the commands you see in
that tutorial.
Based on the error messages you've been giving here, you no longer have an
Amber installation problem. You have an Amber using problem. I highly
recommend that you step back from the MM/PBSA tutorial and start with one
that is a little simpler. The first basic tutorial actually walks you
through using the command-line in Linux, and would be a useful place to
start. See here: http://ambermd.org/tutorials/basic/tutorial0/
Hopefully mastering that tutorial should help you complete the one for
MM/PBSA.
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) .
This line in the tutorial is (very) outdated, and you can ignore it.
Apologies for the confusion, and thanks for the report (I actually just
removed this text from the tutorial so it won't cause further confusion).
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
>
Again, don't do this. Put all of the files for running the tutorial in the
directory you plan to run in. Do *not* run in the amber14 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
>
If you are really new to Amber *and* Linux, then you are starting too
advanced. The computer is like any other instrument -- you need to develop
proficiency using it on basic tasks before you can hope to apply it to more
complex research. I believe that the complexity of your initial task is
making it difficult to learn how to use computational chemistry software
effectively. I highly recommend starting with an easier tutorial, like the
initial basic tutorial B0.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 13 2015 - 14:30:03 PDT
