Re: [AMBER] mmpbsa conflict with Ca2+ ?

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 12 Mar 2015 08:32:59 -0400

On Thu, Mar 12, 2015 at 4:31 AM, Jinfeng Huang <wwsshhjjff00.163.com> wrote:

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> At 2015-03-12 10:35:09, "Jinfeng Huang" <wwsshhjjff00.163.com> wrote:
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> At 2015-03-12 00:21:45, "Jason Swails" <jason.swails.gmail.com> wrote:
> >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
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> Dear amber users,
> Thanks for your suggestions.
> I performed a PB calculation without adding solvate portion, and the
> Ca2+ bellows to the ligand. The _MMPBSA_complex_gb.mdout.0 file warns as
> follows:
> =================== ERROS ==================
> Using carbon SA parms for atom type 3C
> Using carbon SA parms for atom type 2C
> Using carbon SA parms for atom type KA
> Using carbon SA parms for atom type KA
> Using carbon SA parms for atom type KA
> =======================================
> What cause the erro above?
> Should I need to change the strip_mask parameters?
>
> Jingfeng Huang
>
>
>
>
> I have made an mistake, the warning I metioned above was caused by the GB
> caculation, what can I do to solve it ?
>

‚ÄčThose are just warnings. sander doesn't know what kinds of atoms "3C",
"2C", and "KA" are, so it just assumes they have the same radius as carbons
when defining the molecular surface. For a small number of atoms, this
does not really matter (in my opinion). In any case, this is not causing
your calculation to crash. Look for actual *errors* that prevent you from
getting an answer.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 12 2015 - 06:00:04 PDT
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