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
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>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
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Received on Wed Mar 11 2015 - 20:00:02 PDT
