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!
Exiting. All files have been retained.
herbert.herbert-Inspiron-3421:~/Escritorio/amber14/docking1$
______________________________________________________
May be is a simple mistake, but I could not find what it is.
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, inp=1,
/________________________________
I will appreciate your help.
Thank you very much
Best regards,
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*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 18 2014 - 18:30:02 PST
