Re: [AMBER] Fwd: InputError when running MMBPSA.py

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 22 Nov 2014 00:49:30 -0500

I responded to this same email over a week ago. Please check your filters and spam folders to make sure you receive emails from the Amber mailing list.

The answer should be stored in the archives of the mailing list that you can find at archive.ambermd.org.

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
> On Nov 21, 2014, at 10:28 PM, HERBERT MAX VENTHUR PE¥A <h.venthur01.ufromail.cl> wrote:
> 
> Dear Amber Users
> 
> I tried 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 but in .top format
> (solvated.top, complex.top, receptor.top and ligand.top).
> 
> When I 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!
> Exiting. All files have been retained.
> herbert.herbert-Inspiron-3421:~/Escritorio/amber14/docking1$
> 
> ______________________________________________________
> 
> I attached next the input file (*mmpbsa.in <http://mmpbsa.in>*) as well:
> _____________________________________
> 
> &general
> 
>  startframe=100, endframe=250, keep_files=2,
> 
>  verbose=1, entropy=0, netcdf=1
> 
> /
> 
> &pb
> 
>  istrng=100,
> 
> /________________________________
> 
> Is the mmpbsa.in file wrong?
> I will appreciate your help
> 
> Best wishes
> Herbert
> 
> 
> 
> *--Herbert Venthur PeñaProfesor de Estado en Ciencias con Mención en
> Química*
> 
> *Estudiante de Doctorado en Ciencias de Recursos Naturales*
> *Laboratorio de Química Ecológica*
> *Departamento de Ciencias Químicas y Recursos Naturales*
> 
> 
> *Universidad de La FronteraTemuco, Chile*
> *08-3104992*
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Received on Fri Nov 21 2014 - 22:00:02 PST