backward.py fails with "list index out of range"
- scm177
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6 years 4 months ago #7428
by scm177
backward.py fails with "list index out of range" was created by scm177
I have a system that has two types of peptides in a box.
The command I run (with output) is below:
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_charmm.gro -to gromos54a7 -p topol.top
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_charmm.gro -to gromos54a7 -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f CG_FF_FNF_Assembly.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos54a7
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
file:///home/scm177/Backmapping/backward/topol.top
The command I run (with output) is below:
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_charmm.gro -to gromos54a7 -p topol.top
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_charmm.gro -to gromos54a7 -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f CG_FF_FNF_Assembly.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos54a7
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
file:///home/scm177/Backmapping/backward/topol.top
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- riccardo
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6 years 4 months ago #7437
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
Are you sure you have all the mapping files (martini to gromos54a7) for the molecules you want to backmap in the "Mapping" directory?
Also, why would you call your atomistic gromos coordinates "aa_charmm.gro"? :-)
Also, why would you call your atomistic gromos coordinates "aa_charmm.gro"? :-)
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- scm177
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6 years 4 months ago - 6 years 4 months ago #7440
by scm177
Replied by scm177 on topic backward.py fails with "list index out of range"
Hi Riccardo,
thanks for your response.
Yes I do: the only "molecules" in the system are Phe and Asn residues. The system is essentially chains of Fx-Ny peptide chains. As far as I can tell, phe.<forcefield>.map and asn.<forcefield>.map are standard in all mapping files...Please assist.
About naming it aa_charmm: ah yes. Didn't notice it, was trying to get the backmapping to work :)
thanks for your response.
Yes I do: the only "molecules" in the system are Phe and Asn residues. The system is essentially chains of Fx-Ny peptide chains. As far as I can tell, phe.<forcefield>.map and asn.<forcefield>.map are standard in all mapping files...Please assist.
About naming it aa_charmm: ah yes. Didn't notice it, was trying to get the backmapping to work :)
Last edit: 6 years 4 months ago by scm177.
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- riccardo
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6 years 4 months ago #7441
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
Checking the mapping files provided with backward, I see that both phe and asn have indeed a gromos mapping file (i.e., phe.gromos.map and asn.gromos.map). However, if you look in, for example, phe.gromos.map, you'll see:
As you can see, in the [ mapping ] section the string which appears is "gromos", and not "gromos54a7". I'm afraid that backward is not clever enough. Can you try if the following command works:
An alternative would be to add the string "gromos54a7" to the mapping file section [ mapping ], as done below:
[ molecule ]
PHE
[ martini ]
BB SC1 SC2 SC3
[ mapping ]
gromos
...As you can see, in the [ mapping ] section the string which appears is "gromos", and not "gromos54a7". I'm afraid that backward is not clever enough. Can you try if the following command works:
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_gromos.gro -to gromos -p topol.topAn alternative would be to add the string "gromos54a7" to the mapping file section [ mapping ], as done below:
[ molecule ]
PHE
[ martini ]
BB SC1 SC2 SC3
[ mapping ]
gromos gromos54a7
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- scm177
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6 years 4 months ago #7442
by scm177
Replied by scm177 on topic backward.py fails with "list index out of range"
Hi again Riccardo,
I get the same error. Unsure why this is happening.
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_gromos.gro -to gromos -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f CG_FF_FNF_Assembly.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
I get the same error. Unsure why this is happening.
./initram-v5.sh -f CG_FF_FNF_Assembly.gro -o aa_gromos.gro -to gromos -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f CG_FF_FNF_Assembly.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
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- riccardo
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6 years 4 months ago #7443
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
Alright, last things then:
(1) does the backmapping of a single peptide work? or even of a single amino acid (let's say "phe") just taken out of your system (i.e., delete everything but the peptide or amino acid beads) work?
(2) share the files with me (r [dot] alessandri [at] rug [dot] nl), I'll have a look
(1) does the backmapping of a single peptide work? or even of a single amino acid (let's say "phe") just taken out of your system (i.e., delete everything but the peptide or amino acid beads) work?
(2) share the files with me (r [dot] alessandri [at] rug [dot] nl), I'll have a look
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- scm177
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6 years 4 months ago #7444
by scm177
Replied by scm177 on topic backward.py fails with "list index out of range"
Hi again,
1) Executing for a single peptide does not work either.
./initram-v5.sh -f singlepeptide.gro -o aa_gromos.gro -to gromos -p topol.top
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f singlepeptide.gro -o aa_gromos.gro -to gromos -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f singlepeptide.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
2) Emailing you the files shortly, thank you for assisting!
1) Executing for a single peptide does not work either.
./initram-v5.sh -f singlepeptide.gro -o aa_gromos.gro -to gromos -p topol.top
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f singlepeptide.gro -o aa_gromos.gro -to gromos -p topol.top
Checking dependencies:
backward.py ... /home/scm177/Backmapping/backward/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/scm177/Backmapping/backward/backward.py -f singlepeptide.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/scm177/Backmapping/backward/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/scm177/Backmapping/backward/backward.py", line 411, in __init__
crsp.append(crsp[-1])
IndexError: list index out of range
2) Emailing you the files shortly, thank you for assisting!
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- riccardo
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6 years 4 months ago #7456
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
The error is related with backward's backbone reconstruction breaking for a dipeptide (there's no cross product for a C-alpha triplet). We (i.e., Tsjerk & Co) are working on fixing this.
In the meantime, there's a workaround: renaming the BB (backbone) beads to, say, XX. So, for example, one can create a copy of phe.charmm36.map - let's name it fhe.charmm36.map - where the BB beads are renamed XX (and PHE became FHE). So, whenever part of a dipeptide, one should use the FHE phenylalanine (and something similar for the other eventual amino acid involved). Whenever part of a at-least-3-units-long amino acid, you can use the PHE phenylalanine (and all the other amino acids), as usual. Just make sure to change beads and residues names consistently in all the files involved.!
In the meantime, there's a workaround: renaming the BB (backbone) beads to, say, XX. So, for example, one can create a copy of phe.charmm36.map - let's name it fhe.charmm36.map - where the BB beads are renamed XX (and PHE became FHE). So, whenever part of a dipeptide, one should use the FHE phenylalanine (and something similar for the other eventual amino acid involved). Whenever part of a at-least-3-units-long amino acid, you can use the PHE phenylalanine (and all the other amino acids), as usual. Just make sure to change beads and residues names consistently in all the files involved.!
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- rituparna@22
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5 years 2 weeks ago #8070
by rituparna@22
Replied by rituparna@22 on topic backward.py fails with "list index out of range"
Hello Sir
I am working on gromacs 5.0.7. I have prepared an N-terminal capped phenylalanine as the single-peptide. I have created a box with 145 number of the above peptide present in it for self-aggregation. After simulation (output file is sim.gro),I want to backmap it with backward.py and initram.sh files. I have used the most up-to-date backward scripts and used the command-
./initram.sh -f sim.gro -o aa_gromos.gro -to gromos -p topol.top
But the following error is being shown-
initram.sh version 0.1:
(c)2014 Tsjerk A. Wassenaar, PhD
Computational Biology
Friedrich-Alexander University Erlangen-Nuernberg
Staudstrasse 5
91058 Erlangen
Germany
Now executing...
./initram.sh -f sim.gro -o aa_gromos.gro -to gromos -p topol.top
GROMACS VERSION: 5 0 7
MPI: false
/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py -f sim.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 662, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 338, in __init__
b = [float(i) for i in lines[n].split()] + 6*[0] # Padding for rectangular boxes
IndexError: list index out of range
How to debug this?
I am working on gromacs 5.0.7. I have prepared an N-terminal capped phenylalanine as the single-peptide. I have created a box with 145 number of the above peptide present in it for self-aggregation. After simulation (output file is sim.gro),I want to backmap it with backward.py and initram.sh files. I have used the most up-to-date backward scripts and used the command-
./initram.sh -f sim.gro -o aa_gromos.gro -to gromos -p topol.top
But the following error is being shown-
initram.sh version 0.1:
(c)2014 Tsjerk A. Wassenaar, PhD
Computational Biology
Friedrich-Alexander University Erlangen-Nuernberg
Staudstrasse 5
91058 Erlangen
Germany
Now executing...
./initram.sh -f sim.gro -o aa_gromos.gro -to gromos -p topol.top
GROMACS VERSION: 5 0 7
MPI: false
/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py -f sim.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Traceback (most recent call last):
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 662, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 338, in __init__
b = [float(i) for i in lines[n].split()] + 6*[0] # Padding for rectangular boxes
IndexError: list index out of range
How to debug this?
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- riccardo
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5 years 2 weeks ago #8072
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
Hi,
Can you successfully backmap one single peptide?
Can you successfully backmap one single peptide?
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- rituparna@22
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5 years 2 weeks ago #8073
by rituparna@22
Replied by rituparna@22 on topic backward.py fails with "list index out of range"
Hello Sir
No I cannot even backmap one single peptide. My peptide is N-capped (by F-moc group) phenylalanine. I used the following command-
./initram.sh -f phenylalanine.pdb -o aa_gromos.gro -to gromos -p topol.top
But the following error showed-
initram.sh version 0.1:
(c)2014 Tsjerk A. Wassenaar, PhD
Computational Biology
Friedrich-Alexander University Erlangen-Nuernberg
Staudstrasse 5
91058 Erlangen
Germany
Now executing...
./initram.sh -f phenylalanine.pdb -o aa_gromos.gro -to gromos -p topol.top
GROMACS VERSION: 5 0 7
MPI: false
/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py -f phenylalanine.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Non-invertable box. Not able to unbreak molecules...
Traceback (most recent call last):
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 662, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 425, in __init__
d12.append(d12[-1])
IndexError: list index out of range
No I cannot even backmap one single peptide. My peptide is N-capped (by F-moc group) phenylalanine. I used the following command-
./initram.sh -f phenylalanine.pdb -o aa_gromos.gro -to gromos -p topol.top
But the following error showed-
initram.sh version 0.1:
(c)2014 Tsjerk A. Wassenaar, PhD
Computational Biology
Friedrich-Alexander University Erlangen-Nuernberg
Staudstrasse 5
91058 Erlangen
Germany
Now executing...
./initram.sh -f phenylalanine.pdb -o aa_gromos.gro -to gromos -p topol.top
GROMACS VERSION: 5 0 7
MPI: false
/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py -f phenylalanine.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Non-invertable box. Not able to unbreak molecules...
Traceback (most recent call last):
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 662, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/anish-ritu/RITUPARNA/backward-v5/new-github/Backward-master/backward.py", line 425, in __init__
d12.append(d12[-1])
IndexError: list index out of range
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- riccardo
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5 years 2 weeks ago - 5 years 2 weeks ago #8074
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
As you can't backmap even a single peptide, I would guess that there must be some serious problem with your Mapping file and/or atomistic topology. I would first make sure that that's not the case.
The next suspect is the message "Non-invertable box. Not able to unbreak molecules...". Not sure I ever got this error message. Just to explore, though, what are the dimensions of your box? Is it cubic?
The next suspect is the message "Non-invertable box. Not able to unbreak molecules...". Not sure I ever got this error message. Just to explore, though, what are the dimensions of your box? Is it cubic?
Last edit: 5 years 2 weeks ago by riccardo.
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- rituparna@22
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5 years 2 weeks ago #8075
by rituparna@22
Replied by rituparna@22 on topic backward.py fails with "list index out of range"
Yes it is cubic. 13 nm x 13nm x 13nm. I have inserted 300 peptides in it and solvated it with standard CG water.
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- riccardo
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5 years 2 weeks ago #8076
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
Right, but did you check the Mapping and/or atomistic atomistic topology? Do they match? Are you using standard mappings provided with backward?
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3 years 11 months ago #8506
by shashank
Replied by shashank on topic backward.py fails with "list index out of range"
Hello,
I am curious if i can get some help in backmapping my system to AA. I followed the aquaporin tutorial which worked perfectly fine. Along the same lines, i tried to convert the last frame of my CG trajectory but i am getting "list index out of range".
System details: I am working with a homotrimer with some unresolved regions (mostly loops). Bilayer constains POPC/CHOL.
I took the final gro file and executed:
./initram-v5.sh -f step7.1_production.gro -o aa_charmm.gro -to charmm36 -p system.top
Here is the output:
Checking dependencies:
backward.py ... /Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py
gmx ... /usr/local/bin/gmx
/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py -f step7.1_production.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p system.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36
Vendor: continuum
Product: anaconda
Message: trial mode expires in 20 days
Traceback (most recent call last):
File "/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py", line 651, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py", line 417, in __init__
d12.append(d12[-1])
IndexError: list index out of range
I also tried converting a single amino acid in my file but it didnt work. As far as mapping is considered i downloaded it from: aquaporin tutorial and i have CHOL.itp file in the folder.
Thanks
Shashank
I am curious if i can get some help in backmapping my system to AA. I followed the aquaporin tutorial which worked perfectly fine. Along the same lines, i tried to convert the last frame of my CG trajectory but i am getting "list index out of range".
System details: I am working with a homotrimer with some unresolved regions (mostly loops). Bilayer constains POPC/CHOL.
I took the final gro file and executed:
./initram-v5.sh -f step7.1_production.gro -o aa_charmm.gro -to charmm36 -p system.top
Here is the output:
Checking dependencies:
backward.py ... /Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py
gmx ... /usr/local/bin/gmx
/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py -f step7.1_production.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p system.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36
Vendor: continuum
Product: anaconda
Message: trial mode expires in 20 days
Traceback (most recent call last):
File "/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py", line 651, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/Users/shashankpant/Desktop/Research-PPT-Emad/Glt/CG/backward.py", line 417, in __init__
d12.append(d12[-1])
IndexError: list index out of range
I also tried converting a single amino acid in my file but it didnt work. As far as mapping is considered i downloaded it from: aquaporin tutorial and i have CHOL.itp file in the folder.
Thanks
Shashank
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- riccardo
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3 years 11 months ago #8521
by riccardo
Replied by riccardo on topic backward.py fails with "list index out of range"
I never remember what this (cryptic) error message is about.
Not even one single amino acid (in an empty box?) works? Just to make sure, the "system.top" is the atomistic topology, right?
Not even one single amino acid (in an empty box?) works? Just to make sure, the "system.top" is the atomistic topology, right?
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- cneale
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3 years 11 months ago #8526
by cneale
Replied by cneale on topic backward.py fails with "list index out of range"
I think this is a standard python error message that the code is trying to access a list element that is beyond the length of the list. I have encountered this error before while using backward.py when I was using a modified residue for which there was not a corresponding map file in the Mapping/ directory. In my case, adding the needed map file solved the issue. Here, that required map file could be a cap residue (e.g., the script package doesn't ship with a map file for a C-terminal NMA cap).
I am not sure why in my case this wasn't picked up by other tests in the script, but my best guess is that the script found and used a partial match of residue name and then there were not the expected number of atoms.
I am not sure why in my case this wasn't picked up by other tests in the script, but my best guess is that the script found and used a partial match of residue name and then there were not the expected number of atoms.
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- larryhems
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3 years 7 months ago #8718
by larryhems
This error basically means you are trying to access a value at a List index which is out of bounds i.e greater than the last index of the list or less than the least index in the list. So the first element is 0, second is 1, so on. So if there are n elements in a python list , the last element is n-1 . If you try to access the empty or None element by pointing available index of the list, then you will get the "List index out of range " error. To solve this error, you should make sure that you're not trying to access a non-existent item in a list.
Replied by larryhems on topic backward.py fails with "list index out of range"
shashank wrote: IndexError: list index out of range
This error basically means you are trying to access a value at a List index which is out of bounds i.e greater than the last index of the list or less than the least index in the list. So the first element is 0, second is 1, so on. So if there are n elements in a python list , the last element is n-1 . If you try to access the empty or None element by pointing available index of the list, then you will get the "List index out of range " error. To solve this error, you should make sure that you're not trying to access a non-existent item in a list.
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- Saman Fatihi
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1 year 8 months ago #9450
by Saman Fatihi
Replied by Saman Fatihi on topic backward.py fails with "list index out of range"
I am trying to backmap protein from CG to AA using the backward.py script, the protein has a modified residue at GLY residue which is lipidated by a PE-tail. I have added the corresponding .map file in the Mapping/ directory which I created taking POPE and GLY map files as a reference. but I keep getting an error message (I will paste it below), can anyone help or tell me how to fix this?
The back mapping works fine without the modified residue, so I am guessing there is a problem with the created map file. I have matched the atoms in the topology file and map file.
#Command
python2 backward.py -f GLP-CG.gro -raw projected1.gro -o 0-backward1.gro -kick 0.05 -sol -p GLP-topol.top -po backmapped1.top -n backmapped1.ndx -from martini -to charmm36
#Error
Traceback (most recent call last):
File "backward.py", line 685, in <module>
struc = Structure(options["-f"].value, strict=options["-strict"].value)
File "backward.py", line 434, in __init__
d12.append(d12[-1])
IndexError: list index out of range
The back mapping works fine without the modified residue, so I am guessing there is a problem with the created map file. I have matched the atoms in the topology file and map file.
#Command
python2 backward.py -f GLP-CG.gro -raw projected1.gro -o 0-backward1.gro -kick 0.05 -sol -p GLP-topol.top -po backmapped1.top -n backmapped1.ndx -from martini -to charmm36
#Error
Traceback (most recent call last):
File "backward.py", line 685, in <module>
struc = Structure(options["-f"].value, strict=options["-strict"].value)
File "backward.py", line 434, in __init__
d12.append(d12[-1])
IndexError: list index out of range
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- cneale
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1 year 8 months ago #9451
by cneale
Replied by cneale on topic backward.py fails with "list index out of range"
1. can you post your mapping file and one PDB/gro entry for this residue?
2. does the name in the [ molecule ] section match correctly?
3. is the [ martini ] section complete?
4. if you remove your new mapping file, then do you get the exact same error ? (in this case, the original issue might be because misnaming is leading your mapping file to be not found at all rather than that it is found but incorrect).
2. does the name in the [ molecule ] section match correctly?
3. is the [ martini ] section complete?
4. if you remove your new mapping file, then do you get the exact same error ? (in this case, the original issue might be because misnaming is leading your mapping file to be not found at all rather than that it is found but incorrect).
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