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.
>
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Received on Sun Dec 13 2015 - 06:30:04 PST
