Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander

From: Jan-Philip Gehrcke <>
Date: Fri, 31 Aug 2012 15:50:32 +0200

On 08/29/2012 04:17 PM, Jason Swails wrote:
> To be honest, I'm not sure where the error is coming from. Error messages
> in this case seem to be swallowed up (unless they aren't -- are there any
> errors printed out in the _MMPBSA_complex_pb.mdout.0 file?).

This is the whole content of this mdout file:

> Reading parm file (../../complex_unsolvated.prmtop)
> title:
> mm_options: e_debug=3
> mm_options: ipb=2
> mm_options: inp=2
> mm_options: epsin=1.000000
> mm_options: epsout=80.000000
> mm_options: smoothopt=1
> mm_options: istrng=0.000000
> mm_options: radiopt=1
> mm_options: dprob=1.400000
> mm_options: iprob=2.000000
> mm_options: npbopt=0
> mm_options: solvopt=1
> mm_options: accept=0.001000
> mm_options: maxitn=1000
> mm_options: fillratio=4.000000
> mm_options: space=0.500000
> mm_options: nfocus=2
> mm_options: fscale=8
> mm_options: bcopt=5
> mm_options: eneopt=2
> mm_options: cutnb=0.000000
> mm_options: sprob=0.557000
> mm_options: cavity_surften=0.037800
> mm_options: cavity_offset=-0.569200
> Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
> Processing frame 1
> iter Total bad vdW elect nonpolar EPB frms
> eff.c(2660) enb14 --> 481.891
> eff.c(2661) eel14 --> 4625.482

> There were
> significant changes to PBSA, and my guess is you're hitting a bomb in the
> code that is forcing a bail-out. Since the PBSA code used by sander and
> NAB are the same, I would not expect use_sander to fix this.
> The best bet, IMO, would be to run the energy calc for your complex by
> hand, and see if is inadvertently squashing the error message (in
> which case, this should be fixed). The command for PB should be:
> mmpbsa_py_energy -O -i _MMPBSA_pb.mdin -p <complex_prmtop> -c
> _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> (mdcrd replaced by nc if you use netcdf intermediates).
> I'd be interested to see what you learn.

You were right about swallowed error messages. We learned something :-).

> $ mmpbsa_py_energy -i _MMPBSA_pb.mdin -p ../../complex_unsolvated.prmtop -c _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> PB Bomb in pb_aaradi(): No radius assigned for atom 2021 C1 CG

In this case, the error message is printed to stdout by
mmpbsa_py_energy. Of course, MMPBSA should catch stdout and standard
error of this subprocess and make it accessible.

Furthermore, I think the programs in Amber(Tools) should be more
consistent about where they write error messages. I think, as most
people rely on the 'mdout' files in terms of Amber, they should contain
all information. Additional printing to stderr can't hurt.

Now, what does this error message tell us? Could this error be

Thanks for your support!


> All the best,
> Jason

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Received on Fri Aug 31 2012 - 07:00:06 PDT
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