Hi,
I am trying to calculate the binding energy using MMPSA.py with a
protein-dna complex
the command i used
*MMPBSA.py -sp complex_solvated_bz.prmtop -cp complex_nonsolvated_bz.prmtop
-rp protein.prmtop -y prod_trail.mdcrd -i mmpsa.in <
http://mmpsa.in> *
Error I encountered :
*Loading and checking parameter files for compatibility... File
"/usr/local/amber14/bin/MMPBSA.py", line 94, in <module>
app.loadcheck_prmtops() File "/usr/local/amber14/bin/MMPBSA_mods/main.py",
line 572, in loadcheck_prmtops FILES.receptor_prmtop,
FILES.ligand_prmtop) File
"/usr/local/amber14/bin/MMPBSA_mods/parm_setup.py", line 102, in
__init__ self.ligand_prmtop = LoadParm(ligand_prmtop) File
"/usr/local/amber14/bin/chemistry/amber/readparm.py", line 59, in
LoadParm parm = parm.view(AmberParm) File
"/usr/local/amber14/bin/chemistry/amber/amberformat.py", line 223, in
view return cls.load_from_rawdata(self) File
"/usr/local/amber14/bin/chemistry/amber/_amberparm.py", line 156, in
load_from_rawdata inst.initialize_topology() File
"/usr/local/amber14/bin/chemistry/amber/_amberparm.py", line 69, in
initialize_topology self._fill_res_container() File
"/usr/local/amber14/bin/chemistry/amber/_amberparm.py", line 631, in
_fill_res_container for i in
range(self.parm_data['POINTERS'][NRES]-1):KeyError: 'POINTERS'Exiting. All
files have been retained.*
The program didn't create any output files.
However upon using the command
*MMPBSA.py -sp complex_solvated_bz.prmtop -cp
complex_nonsolvated_bz.prmtop -y prod_trail.mdcrd -i mmpsa.in
<
http://mmpsa.in> *
I excluded the receptor/ligand prmtop from the command and the program
worked but the output had only values for complex.
I tried to give the ligand mask in the input file, however, the program
have over written the ligand mask.
Here is the input file:
*&general startframe=1, endframe=100, interval=5 ,keep_files=1,
verbose=2, /&gb igb=2, saltcon=0.10, surften=0.005,/*
I understand to some extent that there is some problem with receptor/ligand
prmtop file. So I had used ante-MMPSA.py to generate the ligand and
receptor files from the compelx prmtop file. I used these newly generated
files to run the energy calculations and it still showed the same error
Any help would be appreciated.
Thanks
Praneeth.
--
*Regards, *
*Praneeth Bommisetti, *
*Fourth year Undergraduate,*
*Integrated M.Sc Chemistry, *
*Indian Institute of Technology Bombay.*
*T: +918424815358, id:praneeth.b.iitb.ac.in <id%3Apraneeth.b.iitb.ac.in>*
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Received on Tue Apr 18 2017 - 14:30:03 PDT
