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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Received on Thu Apr 02 2015 - 06:00:03 PDT
