Dear Sir,
Many thanks for your response. I have attached the file
"_MMPBSA_complex_gb.mdout.0
file" and I didn't find the specific error. I also attached the same in
attachment.
But in error file, it has been written that "bad atom type for Br".
Error:
bad atom type: br
> File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA.py.MPI", line 96,
in
> <module>
> app.run_mmpbsa()
> File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py", line
> 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py", line
> 148, in run
> self.prmtop))
> CalcError: /cbio/jclab/projects/collab/amber14/bin/sander failed with
> prmtop com.top!
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
Thanks & regards
*Ramesh M*
Email: shreeramesh.gmail.com
Mobile: (91) + 9646469938 (27) + (0) 844556164
On Thu, Apr 2, 2015 at 5:40 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Apr 2, 2015 at 3:00 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
>
> > Dear All,
> >
> > I ran a tleap for the protein and combined with the ligand using the
> script
> > named "tleap.all" in AMBER12. The script of tleap as follows
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > LIG = loadmol2 LIG.mol2
> > loadamberparams LIG.frcmod
> > check LIG
> > receptor = loadPDB rec.pdb
> > complex = combine {receptor LIG}
> > set default PBRadii mbondi2
> > saveAmberParm LIG LIG.top LIG.crd
> > saveAmberParm receptor rec.top rec.crd
> > saveAmberParm complex com.top com.crd
> > savepdb complex complex_gas.pdb
> > charge complex
> > addIons2 complex Cl- 0
> > solvateBox complex TIP3PBOX 10.0
> > saveAmberParm complex com_solvated.top com_solvated.crd
> > savepdb complex com_solvated.pdb
> > quit
> >
> > The log file of tleap is enclosed in attachment. Further I ran md in
> > AMBER14 and was successful for 5ns. Further I ran MMPBSA using the script
> > named "mmpbsa.in and mmpbsa_SUB" (enclosed in attachment) in AMBER14
> and I
> > got the following error for "com.top" (enclosed in attachment) which was
> > generated while running the script "tleap.all". Can you please guide me
> to
> > solve this problem in calculating binding free energies?
> >
> > Error:
> >
> >
> > ligand comples using the
> >
> > bad atom type: br
> > File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA.py.MPI", line 96,
> in
> > <module>
> > app.run_mmpbsa()
> > File "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/main.py",
> line
> > 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> > "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 79, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> > "/cbio/jclab/projects/collab/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 148, in run
> > self.prmtop))
> > CalcError: /cbio/jclab/projects/collab/amber14/bin/sander failed with
> > prmtop com.top!
> > Exiting. All files have been retained.
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >
>
> ​Look at the _MMPBSA_complex_gb.mdout.0 file. There should hopefully be an
> error message there that is more enlightening.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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>
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Received on Thu Apr 02 2015 - 08:00:03 PDT
