Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Tue, 10 Jun 2014 11:08:01 -0700 (PDT)

I am attaching the output file from AmberTools14.  Yes I could see some errors with the new version ! ------------------------------------------------------------------------------ CalcError: /amber14_gpu/amber14/bin/mmpbsa_py_energy failed with prmtop complexK4M3.prmtop!     PB Bomb in pb_aaradi(): No radius assigned for atom  1006  D1    DZ ------------------------------------------------------------------------------ I also notice that both Zn and Dummy atoms were removed in the complex.pdb file. partial output from _MMPBSA_complex_gb.mdout.0 (please see the attached file) -------------------------------------------------------------- Reading parm file (complexK4M3.prmtop) title:                                                                                     mm_options:  e_debug=2     mm_options:  gb=5     mm_options:  rgbmax=25.000000     mm_options:  gbsa=1     mm_options:  surften=0.007200     mm_options:  cut=999.000000     mm_options:  epsext=78.300000     mm_options:  kappa=0.127315 Using carbon SA parms for atom type ZN Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ Using carbon SA parms for atom type ZN Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ Using carbon SA parms for atom type DZ bad number of bonds to N3: 1072 4; using default nitrogen parameters -------------------------------------------------------------------------- It seems that the parameters for Zn and DZ are not taken up from prmtop files?. Please suggest me the solution. Thanks, Senthil On Tuesday, June 10, 2014 1:08 PM, Jason Swails <jason.swails.gmail.com> wrote: I don't see any error message there, either. Without some sort of error message from the program computing the energies (sander or mmpbsa_py_energy), it will be impossible to diagnose. That said, your output file showed you are using Amber 11.  Please update to AmberTools 14, as we can really only support the latest version of AmberTools (especially since it is FOSS). HTH, Jason On Tue, Jun 10, 2014 at 12:53 PM, Senthil Natesan <sen.natesan@yahoo.com> wrote: > Jason, > > I am attaching the file here. I do not see any obvious errors written > though. Please point me  to the error. > > Thanks, > > Senthil > > >  On Tuesday, June 10, 2014 12:26 PM, Jason Swails <jason.swails@gmail.com> > wrote: > > > On Tue, Jun 10, 2014 at 11:57 AM, Senthil Natesan <sen.natesan@yahoo.com> > wrote: > > > Thank you Jason. > > > > I am running GB, PB and NMode analysis as well. > > > > > > The input file is: > > > > &general > >  startframe=50, endframe=99999, interval=100, > >  verbose=2, > > > > / > > &gb > >  igb=5, saltcon=0.150, > > / > > &pb > >  istrng=0.15, > > / > > &nmode > >  nmstartframe=50, nmendframe=99999, nminterval=100, > >  maxcyc=50000, drms=0.0001, > > / > > > > I submitted the job with the following input command: > > > > MMPBSA.py -O -i mmpbsa.in  -o mmpbsa.out -sp complex_solvated.prmtop -cp > > complex.prmtop -rp protein.prmtop -lp peptide.prmtop -y > > complex_solvated_prod1.mdcrd complex_solvated_prod2.mdcrd > > > > > > The calculation ran successfully for the ligand (peptide), but failed for > > both complex and receptor as both contains Zn. The error message is > > > > Error: No potential terms in sander output ! Check output files. > > > > ​You need to check the output files (e.g., _MMPBSA_complex_gb.mdout.0) for > the real error messages. > > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Tue Jun 10 2014 - 11:30:02 PDT
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