The file is in CSV (comma separated values) format. You should be able to
open it in a number of spreadsheet applications using comma delimiters.
This will make the output a lot easier to read.
I hope that helps.
-Bill
On Fri, Jun 1, 2012 at 9:29 AM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi Jason,
> I ran MMPBSA.py.MPI successfully by copying "sander" from
> /home/Amber/amber11/bin to /home/Amber/amber12/bin, so that
> MMPBSA could find sander. I can not be sure whether this is proper.
> However, the output file FINAL_DECOMP_MMPBSA.dat became a mess which
> confused me.
>
> Here is my input file, and I will attach FINAL_DECOMP_MMPBSA.dat in the
> email.
> Per-residue GB and PB decomposition
> &general
> startframe=201, verbose=1,
> strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1,
> dec_verbose=1,
> /
>
> I tried to set dec_verbose=3 and run the job again with -rewrite-output,
> but the program aborted with the following error:
> KeyError: 'rismrun_std'
>
> I compiled the serial vesion of AmberTools 12 with -nofftw3. Will this be
> the case?
> Thanks.
>
> Cao Yang,
> Zhejiang University
>
>
>
>
> At 2012-06-01 20:40:44,"Jason Swails" <jason.swails.gmail.com> wrote:
> >On Fri, Jun 1, 2012 at 12:58 AM, Cao Yang <muxiachuixue.163.com> wrote:
> >
> >> Hi all,
> >>
> >> I installed AMBER11 and AmberTools 12 with all bugfix. In order to
> combine
> >> AMBER11 with AmberTools 12, I did the following commands before running
> >> MMPBSA.py:
> >>
> >> export AMBERHOME=/home/Amber/amber12
> >> export PATH=$PATH:$AMBERHOME/bin:/home/Amber/amber11/bin
> >>
> >> But MMPBSA aborted in my decompostion analysis with the error below:
> >> MMPBSA_Error: Could not find necessary program [sander]
> >>
> >> The reason may be that MMPBSA could not find sander in
> >> /home/Amber/amber12/bin.
> >> But I have added "AMBERHOME/bin:/home/Amber/amber11/bin" to my
> >> environment. Won't MMPBSA search sander in /home/Amver/amber11/bin? That
> >> confused me. This time, I just copy sander from /home/Amber/amber11/bin
> to
> >> /home/Amber/amber12/bin. And the job runs smoothly.
> >>
> >
> >By default, MMPBSA.py only searches in $AMBERHOME/bin for executables,
> >since that's where it expects to find the programs that it is known to
> work
> >with. To search for programs outside this folder (and anywhere in the
> >PATH), add the variable "search_path=1" to the &general section of your
> >MMPBSA.py input file.
> >
> >Also note that you should set dec_verbose=3 to get sander from Amber 11 to
> >work. You can change dec_verbose and run -rewrite-output to get the
> output
> >file you desire, but only dec_verbose=3 will allow the calculation to run
> >in the first place (unless you use -make-mdins, remove the dec_verbose
> >variable from all of the mdin files, then use -use-mdins).
> >
> >HTH,
> >Jason
> >
> >--
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Candidate
> >352-392-4032
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Jun 01 2012 - 08:00:04 PDT
