Re: [AMBER] MMPBSA.py "timer: need to reset the time before start"

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 5 Nov 2012 13:04:23 -0500

Please make sure all bug fixes have been applied.

You can run

cd $AMBERHOME && ./patch_amber.py --update

To do this. Then, reinstall AmberTools 12.

My guess is that you have an error message that is being masked during your pb calculation. One of the bug fixes prints the errors out for you.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 4, 2012, at 9:51 PM, Adelene Sim <adelenes.bii.a-star.edu.sg> wrote:
> Hi, I'm running AMBER 12 and trying to use MMPBSA.py to run some PB 
> calculations but ran into an error ("CalcError: 
> /home/software/amber12/bin/mmpbsa_py_energy failed with prmtop 
> complex.parm7".
> 
> I next ran "mmpbsa_py_energy -i _MMPBSA_pb.mdin -p complex.parm7 -c 
> _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output" and got this 
> error "timer: need to reset the time before start".
> 
> I haven't seen this problem in the Amber list, so am unsure how to fix it.
> 
> Can someone help, please? Thanks!
> 
> Adelene
> 
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Received on Mon Nov 05 2012 - 10:30:02 PST