Hello all
Any anyone answer on above query?
On Sun, Sep 8, 2019 at 1:12 AM shivangi agarwal <
shiviagarwalpharma.gmail.com> wrote:
> Hello all
> I am facing problem in calculation of per residue decomposition energy. I
> am running following command on mdcrd files. The MMGBSA and MMPBSA have
> been successfully completed but the decompostion.dat file is empty and
> following command exits with an error as mentioned below:
>
> *MMPBSA.py -i mmgbsa.in <http://mmgbsa.in> -o explicit.dat -sp
> complex-box.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
> -y ../sim1_clq_complex.mdcrd*
> Loading and checking parameter files for compatibility...
> cpptraj found! Using /home/ravi/anaconda3/bin/cpptraj
> sander found! Using /home/ravi/anaconda3/bin/sander
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
> Running calculations on normal system...
> Beginning GB calculations with /home/ravi/anaconda3/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> Beginning PB calculations with /home/ravi/anaconda3/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> File "/home/ravi/anaconda3/bin/MMPBSA.py", line 109, in <module>
> app.write_final_outputs()
> File
> "/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/main.py",
> line 645, in write_final_outputs
> self.normal_system, self.mutant_system, self.mut_str, self.pre)
> File
> "/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/output_file.py",
> line 673, in write_decomp_binding_output
> gb_bind.parse_all()
> File
> "/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/amber_outputs.py",
> line 2112, in _parse_all_csv
> self._parse_all_begin()
> File
> "/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/amber_outputs.py",
> line 2015, in _parse_all_begin
> com_token = self.com.get_next_term(searched_token, framenum)
> File
> "/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/amber_outputs.py",
> line 1536, in _get_next_term
> internal = float(line[11:20])
> ValueError: could not convert string to float: '*********'
> Exiting. All files have been retained.
> ######mmgbsa.in##### <http://mmgbsa.in#%23%23%23%23>
> Per-residue GB and PB decomposition
> &general
> startframe=1, endframe=20000, verbose=2000,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1, print_res="1-306"
> dec_verbose=1,
> /
> ###########################
>
> Have checked mailing list which suggest the problem occurs with old Amber
> version before 11 but I am already calculating with Ambertools19.
> So, can anyone help me out in finding the problem?
>
> Thanks and regards
> Shivangi Agarwal
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 09 2019 - 08:30:02 PDT
