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.
no i installed new verssion of AmberTools 15 but it also didn't work . kindly help me by giving an example how can i properly install and can run MMPBSA.py i have very little time and i am worried about my project i am unable to understand your instructions easily that you discuss prior so please guide me about these commands by giving me simple demo as its hard for me to get about these commands and i only want to use MMPBSA.py package from AmberTools 15 or 14 .
Regards
Ayesha Kanwal
> Date: Tue, 13 Oct 2015 17:06:10 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> 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 Wed Oct 14 2015 - 02:30:05 PDT
