Shreeramesh,
The error is exactly what it sounds like- you have an atom type (in this
case, a bromine ion I'm guessing) that sander doesn't recognize, so you
need to edit the mdread file for sander and add it in.
The bad atom type Br problem is actually well documented on the mailing
list- this (
http://archive.ambermd.org/201111/0370.html) should find a more
descriptive solution of what you need to specifically change.
Best,
Kenneth
On Thursday, April 2, 2015, Shreeramesh <shreeramesh.gmail.com> wrote:
> 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 <javascript:;>
> Mobile: (91) + 9646469938 (27) + (0) 844556164
>
>
> On Thu, Apr 2, 2015 at 5:40 AM, Jason Swails <jason.swails.gmail.com
> <javascript:;>> wrote:
>
> > On Thu, Apr 2, 2015 at 3:00 AM, Shreeramesh <shreeramesh.gmail.com
> <javascript:;>> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Thu Apr 02 2015 - 08:00:05 PDT
