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 - 19:30:02 PST
