NMRBox qMDD

[Mark]

Hello,

I'm trying to test qMDD on NMRBox (I can't get it to run on my own system) using the gNhsqc_S example data set.

If I run this through the qMDD GUI I get the error:

####> mddnmr4pipeN  1 2 3 42
########## conversion from spectrometer format to nmrPipe format ../b_hnco to ./XYZA/ft4sp.xyza.2D
No fid file ../b_hnco
mddnmr4pipeN 1 2 3 42 failed
Warning: CEXP corrected: new yn old nn
Error command 'FTx.sh.2D ./XYZA/ft4sp.xyza.2D' failed

If I run just proc.sh from the terminal I get a similar, although slightly different error (no reference to b_hnco)

####> mddnmr4pipeN  1 2 3 4 5
########## conversion from spectrometer format to nmrPipe format ../gNhsqc_S.fid to ./XYZA/ft4sp.xyza.2D
No fid file ../gNhsqc_S.fid
Error command 'FTx.sh.2D ./XYZA/ft4sp.xyza.2D' failed

mddnmr4pipeN 1 2 3 4 5 failed

Any help would be much appreciated.

Thanks!

Mark

[Vladislav Orekhov]

Hi Mark,
perhaps, files in  gNhsqc_S.proc dir are corrupted. Please remove or rename this directory and start from selecting the spectrum in qMDD.
The error means that qMDD cannot find file ../gNhsqc_S.fid/fid . So please check that it exists in the path relative to gNhsqc_S.proc dir. Path to ../gNhsqc_S is set at the beginning of proc.sh script.

Regards,
Vladislav

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[Krzysztof Kazimierczuk]

Hi,

If this is gNhsqc_S from mddnmr examples, then I can process it normally (starting from qMDD) on NMRbox. Are you sure that you are choosing gNhsqc_S.fid folder in qMDD?

(Other thing is , that numpy releases warning - qMDD uses older version of numpy. But this should not be a problem)

Regards,
Krzysztof

-- 
Pozdrawiam,
Krzysztof Kazimierczuk<br />


Krzysztof Kazimierczuk, PhD
Laboratory of Intermolecular Interactions
University of Warsaw
Zwirki i Wigury 101, 02-089 Warsaw
tel. +48 22 8220211 ext. 421

[Mark]

Hello,

I'm using the qMDD version on NMRbox (v3). I downloaded the gNhsqc_S dataset from the mddnmr website to test (http://mddnmr.spektrino.com/downloadE/gNhsqc_S_30Jun2011.tgz). On extracting this, there is a folder gNhsqc_S with gNhsqc_S.fid and gNhsqc_S.proc inside. In proc.sh (within gNhsqc_S.proc) I have

setenv FID ../gNhsqc_S.fid

i.e. pointing to the raw data directory.

I also tried deleting the .proc folder and starting from the defaults given by qMDD. Interestingly this gives

setenv FID ../gNhsqc_S

i.e. without the .fid extension

I have also tried putting the full path to the .fid folder.

All of these give the same error for me:

####> mddnmr4pipeN  1 2 3 42
########## conversion from spectrometer format to nmrPipe format ../b_hnco to ./XYZA/ft4sp.xyza.2D
No fid file ../b_hnco
mddnmr4pipeN 1 2 3 42 failed
Warning: CEXP corrected: new yn old nn
Error command 'FTx.sh.2D ./XYZA/ft4sp.xyza.2D' failed

Thanks for your help.

Mark

[Vladislav Orekhov]

Hi Mark,
we traced the problem to scripts proc.sh and recFT.com, which are found both in local processing proc directory and in mddnmr/com
The problem is solved, if  current directory "." stands before ..../mddnmr/com  in the path.

Regards,
Vladislav

On 2017-10-17 11:34, Mark wrote: