Re: [AMBER] mmpbsa conflict with Ca2+ ?

From: Jinfeng Huang <>
Date: Thu, 12 Mar 2015 16:31:01 +0800 (CST)

At 2015-03-12 10:35:09, "Jinfeng Huang" <> wrote:

At 2015-03-12 00:21:45, "Jason Swails" <> wrote:
>On Wed, Mar 11, 2015 at 10:52 AM, Jinfeng Huang <>
>> 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/", line 96, in
>> <module>
>> app.run_mmpbsa()
>> File "/share/apps/", line
>> 218, in run_mmpbsa
>>, self.stdout)
>> File "/share/apps/",
>> line 79, in run
>>, stdout=stdout, stderr=stderr)
>> File "/share/apps/",
>> line 148, in run
>> self.prmtop))
>> CalcError: /share/apps/ failed
>> with prmtop!
>> =====================
>> 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 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.
>Jason M. Swails
>Rutgers University
>Postdoctoral Researcher
>AMBER mailing list

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 ?

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Received on Thu Mar 12 2015 - 02:00:02 PDT
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