Reply on the issue tracker.
On Sun, 13 Dec 2015 16:10:25 +0200
Fabian gmail <fabian.glaser.gmail.com> wrote:
> Dear Hannes,
>
> I run a test TI analysis with AMBER and I installed and I am trying
> to use the alchemical_analysis.py script for the example that comes
> with the with it, from the sampes/amber directory as it is. The
> scripts runs, but I get an error I don’t understand, probably my
> python ignorance, here it is the output, it seems it starts to run,
> but it gives a mbar_lambdas error.
>
>
> /Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber
> 03:24 PM Sun Dec
> 13$ ../../alchemical_analysis/alchemical_analysis.py -a AMBER -d
> data/* -m TI -p ti00* -q out
>
> It seems the script starts to run
>
> Started on Sun Dec 13 15:25:08 2015
>
> Command line was: ../../alchemical_analysis/alchemical_analysis.py -a
> AMBER -d data/0.0 data/0.1 data/0.2 data/0.3 data/0.4 data/0.5
> data/0.6 data/0.7 data/0.8 data/0.9 data/1.0 -m TI -p ti00* -q out
>
> Loading in data from data/0.0/ti002.out... 50 data points, 10 DV/DL
> averages Loading in data from data/0.0/ti003.out... 50 data points,
> 10 DV/DL averages
>
> Sorting input data by starting time and lambda
> Traceback (most recent call last):
> File "../../alchemical_analysis/alchemical_analysis.py", line 1224,
> in <module> main()
> File "../../alchemical_analysis/alchemical_analysis.py", line 1172,
> in main nsnapshots, lv, dhdlt, u_klt = parser_amber.readDataAmber(P)
> File
> "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/parser_amber.py",
> line 582, in readDataAmber if len(dvdl_all) != len(mbar_lambdas):
> UnboundLocalError: local variable 'mbar_lambdas' referenced before
> assignment
>
> Any idea what is happening here?
>
>
> If I use the script run.sh that comes with the installation I get a
> different error:
>
> ./run.sh
> Traceback (most recent call last):
> File "../../alchemical_analysis//alchemical_analysis.py", line
> 1224, in <module> main()
> File "../../alchemical_analysis//alchemical_analysis.py", line
> 1200, in main Deltaf_ij, dDeltaf_ij = estimatewithMBAR(u_kln, N_k,
> P.relative_tolerance, regular_estimate=True) File
> "../../alchemical_analysis//alchemical_analysis.py", line 290, in
> estimatewithMBAR O = MBAR.computeOverlap()[2] IndexError: invalid
> index to scalar
> variable. /Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber
> 03:41 PM Sun Dec 13$ more
> run.sh ../../alchemical_analysis//alchemical_analysis.py \ -a AMBER \
> -d data \
> -p '[01].*/ti00[2-9]' \
> -q out \
> -o . \
> -r 5 \
> -u kcal \
> -s 0 \
> -g \
> -w \
> > run.log
> /Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber
>
>
> Could you please help me understand what I am doing wrong?
>
> Thanks a lot in advance,
>
> Fabian
>
>
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering Technion - Israel Institute of Technology, Haifa 32000,
> ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering Technion - Israel Institute of Technology, Haifa 32000,
> ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
> > On 4 Dec 2015, at 4:21 PM, Hannes Loeffler
> > <Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> > On Fri, 4 Dec 2015 14:09:29 +0200
> > Fabian Glaser <fabian.glaser.gmail.com> wrote:
> >
> >> Thanks a lot!
> >>
> >> So no registration?
> >
> > What is registration?
> >
> >
> >> Just min then heating at constant pressure and
> >> then production at constantvpressure will do it for every lambda?
> >> No volume equilibration necessary?
> >
> > Heating would occur at constant volume. Constant pressure will
> > adjust the volume.
> >
> >
> >> Finally what about your preferred tool for the final analysis for
> >> DG of hydration? I know there are several.
> >
> > I use https://github.com/MobleyLab/alchemical-analysis . I am
> > writing the AMBER parser for this tool. My code is not merged in
> > yet but I hope this to happen today, otherwise:
> > https://github.com/halx/alchemical-analysis for the fork of mine.
> >
> >
> > Cheers,
> > Hannes.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Dec 14 2015 - 02:00:04 PST
