Again, I reinstalled the serial version of amber12 and redo everything i,e
generating .prmtop file using chamber, trajectory conversion from .dcd to
.mdcrd using that .prmtop file and then run the mmpbsa.py and mmpbsa.py.MPI
both.
/home/sudipta/AMBER/amber12/bin/MMPBSA.py -O -i mmpbsa_ptraj.in -o
FINAL_RESULTS_MMPBSA_NMODE.dat -sp 3jzb_complex_solv.prmtop -cp
3jzb_complex.prmtop -y 3jzb_protein_ligand_system_36.mdcrd >
progress_mmpbsa.log
KeyError: 'risumrun'
Exiting. All files have been retained.
I am not clear where from this error is coming. please help me out in this
regard.
On Mon, Sep 23, 2013 at 7:36 PM, sudipta <sudipta.mml.gmail.com> wrote:
> Do I need to download ambertools13. I have not done that. Rather, I ran
> the commands that you mentioned in the previous mail. However, the second
> command line didn't work and I just use the 'make install' for that.
> Moreover, i used -mpi flag in the first command line to install the MPI
> version of that.
>
> However, the MMPBSA.py.MPI program is not running
>
>
> On Mon, Sep 23, 2013 at 2:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Mon, Sep 23, 2013 at 11:59 AM, sudipta <sudipta.mml.gmail.com> wrote:
>>
>> > Hi Jason,
>> >
>> > I have sent all the related files for running the MMPBSA.py.MPI program
>> to
>> > you. Please take a look on those whenever you are free. Also let me
>> know if
>> > you need any further information from my side.
>> >
>>
>> The problem was in the Python parsing of the chamber topology files. I've
>> fixed the issue and the update is now available. If you run the following
>> commands:
>>
>> cd $AMBERHOME && ./configure gnu
>> make -C AmberTools/src/parmed install
>>
>> That should update your installation (the modified 'make' command will
>> install _just_ the ParmEd files -- if more than just update.18 are applied
>> to your installation you should just run "make install" to build
>> everything).
>>
>> HTH,
>> Jason
>>
>> Best
>> > sudipta
>> >
>> >
>> > On Mon, Sep 23, 2013 at 7:04 AM, Jason Swails <jason.swails.gmail.com
>> > >wrote:
>> >
>> > > A couple more comments:
>> > >
>> > > On Sun, Sep 22, 2013 at 7:13 PM, sudipta <sudipta.mml.gmail.com>
>> wrote:
>> > >
>> > > > [snip]
>> > > >
>> > > >
>> > > > Do I need to use ante-MMPBSA.py program for generating the .prmtop
>> > file
>> > > > for running MMPBSA.py.MPI program. If so how do I use that? Is there
>> > any
>> > > > significant difference between AMBERtools12 and AMBERtools13 for
>> > running
>> > > > MMPBSA.py.MPI program
>> > >
>> > >
>> > > No, ante-MMPBSA.py is never necessary if you create all of the needed
>> > > topology files in the beginning, prior to running any calculations
>> (as is
>> > > recommended practice). ante-MMPBSA.py is particularly useful when you
>> > > decide to do MM/PBSA calculations on a system after creating the
>> topology
>> > > file and you don't happen to have the files you need to create them
>> > through
>> > > tleap.
>> > >
>> > > However, ante-MMPBSA.py does _not_ work with chamber-generated
>> topology
>> > > files, so that's not even an option in your case. As for the 12 vs.
>> 13
>> > > difference, AmberTools 13 has more bug fixes and more stable PBSA
>> options
>> > > than AmberTools 12 in terms of the default solvation radii for the
>> > > non-polar solvation free energy part of the calculation.
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> > > --
>> > > Jason M. Swails
>> > > BioMaPS,
>> > > Rutgers University
>> > > Postdoctoral Researcher
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Sep 23 2013 - 17:00:03 PDT
