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SUPER LARGE RNA TO CG
- wind
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4 years 6 months ago #8307
by wind
SUPER LARGE RNA TO CG was created by wind
i tryed to building a model for RNA by martinize-nucleotide.py
first i use TINKER with amber99sb force field
then i want use martinize-nucleotide.py to building CG model
but i got a problem
my RNA have over 120000 atoms
isn't martinize-nucleotide.py this script can't support this RNA ?
first i use TINKER with amber99sb force field
then i want use martinize-nucleotide.py to building CG model
but i got a problem
my RNA have over 120000 atoms
isn't martinize-nucleotide.py this script can't support this RNA ?
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- bart
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4 years 6 months ago #8310
by bart
Replied by bart on topic SUPER LARGE RNA TO CG
Hey there Wind,
I am afraid we need a little bit more information. Could you copy the error you get? A known problem with martinize-nucleotide.py is that its very picky on the exact naming of everything including things like "'". Make sure your RNA is in exactly the same format as the RNA in the turtorial: cgmartini.nl/images/stories/tutorial/201...torials_20170815.tar .
Cheers,
Bart
I am afraid we need a little bit more information. Could you copy the error you get? A known problem with martinize-nucleotide.py is that its very picky on the exact naming of everything including things like "'". Make sure your RNA is in exactly the same format as the RNA in the turtorial: cgmartini.nl/images/stories/tutorial/201...torials_20170815.tar .
Cheers,
Bart
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- wind
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4 years 6 months ago #8312
by wind
Replied by wind on topic SUPER LARGE RNA TO CG
HI bart
here is my error
bigwind@master:~/CG2$ perl aa2cg.pl
:-) GROMACS - gmx editconf, VERSION 5.1.5 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, VERSION 5.1.5
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx editconf -f RNAseq-cleaned.pdb -o RNAseq-cleaned.gro
Read 99999 atoms
No velocities found
gcq#399: "The soul? There's nothing but chemistry here" (Breaking Bad)
INFO MARTINIZE, script version 2.2
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22nucleic forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
File "martinize-nucleotide.py", line 5023, in <module>
main(options)
File "martinize-nucleotide.py", line 4474, in main
chains = [ Chain(options,residuelist[i:j],name=chr(65+k)) for i,j,k in chains ]
ValueError: chr() arg not in range(256)
here print it read 99999 atoms but i have 130000 atoms in my pdb file
and it can't build CG MODEL
but delet some atoms i can pass this script when my RNA onle 6000 atoms
and it can build CG model when it only 6000atoms
bigwind
here is my error
bigwind@master:~/CG2$ perl aa2cg.pl
:-) GROMACS - gmx editconf, VERSION 5.1.5 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, VERSION 5.1.5
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx editconf -f RNAseq-cleaned.pdb -o RNAseq-cleaned.gro
Read 99999 atoms
No velocities found
gcq#399: "The soul? There's nothing but chemistry here" (Breaking Bad)
INFO MARTINIZE, script version 2.2
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22nucleic forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
Traceback (most recent call last):
File "martinize-nucleotide.py", line 5023, in <module>
main(options)
File "martinize-nucleotide.py", line 4474, in main
chains = [ Chain(options,residuelist[i:j],name=chr(65+k)) for i,j,k in chains ]
ValueError: chr() arg not in range(256)
here print it read 99999 atoms but i have 130000 atoms in my pdb file
and it can't build CG MODEL
but delet some atoms i can pass this script when my RNA onle 6000 atoms
and it can build CG model when it only 6000atoms
bigwind
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- bart
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4 years 3 months ago #8409
by bart
Replied by bart on topic SUPER LARGE RNA TO CG
I agree something is off and it seems a limitation of the software. I hope you found your way around it.
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- tsjerk
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4 years 3 months ago #8410
by tsjerk
Replied by tsjerk on topic SUPER LARGE RNA TO CG
I'm sorry I missed this earlier (RNA/DNA is not my field of expertise). This surely points to a bug in the program, but it's also quite a challenge to try and do something with a 130k atoms piece of RNA. If you haven't solved your problem yet, I would be happy to see if I can lend a hand and try and track the issue, hopefully to solve it. I would ask you to provide me the input file, though, so I can use it for testing the program (and maybe see how martinize2 fares).
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