Re: [AMBER] Error with MMPSA.py calculation

From: Jason Swails <jason.swails.gmail.com> Date: Wed, 19 Apr 2017 20:20:59 -0400

--
Jason M. Swails 
> On Apr 18, 2017, at 5:22 PM, Praneeth Bommisetti <iampraneeth11.gmail.com> wrote:
> 
> 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 :
> 
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> *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:
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> *&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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