> On Nov 18, 2014, at 9:16 PM, HERBERT MAX VENTHUR PE¥A <h.venthur01.ufromail.cl> wrote:
>
> Dear All
>
> I've been trying to perform some MMPBSA calculations to get free energy of
> binding in some complexes (ligand-protein). I prepared all the files
> required according to the manual in AmberTools14 (which is the version
> installed in my laptop (ubuntu)). I have the trajectory file of the
> solvated complex in .netcdf, also the topology files prepared through the
> tleap command without any problem (solvated.top, complex.top, receptor.top
> and ligand.top).
>
> Well, the problem is that when I open the terminal and run MMPBSA.py
> according to the tutorial (
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm), it
> says that there is no calculation specified.
>
> *Like this:*
>
> herbert.herbert-Inspiron-3421:~$ cd Escritorio/amber14/
> herbert.herbert-Inspiron-3421:~/Escritorio/amber14$ source amber.sh
> herbert.herbert-Inspiron-3421:~/Escritorio/amber14$ cd docking1
> herbert.herbert-Inspiron-3421:~/Escritorio/amber14/docking1$ MMPBSA.py -O
> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com_solvated.top -cp com.top
> -rp rec.top -lp lig.top -y *.netcdf
> File "/home/herbert/Escritorio/amber14/bin/MMPBSA.py", line 93, in
> <module>
> app.check_for_bad_input()
> File "/home/herbert/Escritorio/amber14/bin/MMPBSA_mods/main.py", line
> 853, in check_for_bad_input
> raise InputError('You did not specify any type of calculation!')
> InputError: You did not specify any type of calculation!
This only happens if your MMPBSA.py input file does not have a &pb, &gb, or &nmode section present, so given the input file below I don’t see how you could possibly be seeing this error.
Are you sure that the mmpbsa.in file that you sent here is the same one that you are using in this example?
Also make sure that the MMPBSA.py tests pass, and see if the input files from those tests work for your system, and mutate the options to match your input file one at a time until you see which one is causing the problems.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 18 2014 - 23:00:04 PST
