On Wed, Mar 11, 2015 at 10:52 AM, Jinfeng Huang <wwsshhjjff00.163.com>
wrote:
> Dear amber users,
> I need to calculate the bingding free energy with a structure
> containing Ca2+ ions. But when I using mmpbsa of amber14,there is some
> erros as follows.
> =================
> calculating complex contribution...
> File "/share/apps/amber14.intel/amber14/bin/MMPBSA.py", line 96, in
> <module>
> app.run_mmpbsa()
> File "/share/apps/amber14.intel/amber14/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/share/apps/amber14.intel/amber14/bin/MMPBSA_mods/calculation.py",
> line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/share/apps/amber14.intel/amber14/bin/MMPBSA_mods/calculation.py",
> line 148, in run
> self.prmtop))
> CalcError: /share/apps/amber14.intel/amber14/bin/mmpbsa_py_energy failed
> with prmtop m0.top!
> =====================
> How should I deal with the problem?
>
​First look at the output from the complex calculation
(_MMPBSA_complex_gb.mdout.0; or pb instead of gb if this is a PB
calculation). Is there an error message there?
Also, if you give MMPBSA.py a solvated prmtop, it automatically strips all
water *and* ions from the trajectory. If you have not changed strip_mask
in the &general section to keep the important Ca2+ ions, then your
calculation will fail.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 11 2015 - 09:30:04 PDT
