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martinize-dna.py
- Fondyffendof
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4 years 1 week ago #8497
by Fondyffendof
martinize-dna.py was created by Fondyffendof
Hi
I ran the tutorial for the ds dna succesfully but switching over to my own structure caused an error while martinizing with python version 2.7.17:
python martinize-dna.py -dnatype ds-stiff -f origami-cleaned.gro -o cg-origami.top -x cg-origami.pdb
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 elnedyn22dna 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-dna.py", line 5070, in <module>
main(options)
File "martinize-dna.py", line 4522, 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)
The origami: origami-cleaned.gro
consist of 84 chains and looks like
162545
1DT5 N1 1 -1.656 -6.096 -17.021
1DT5 C6 2 -1.780 -6.056 -16.978
1DT5 H6 3 -1.857 -6.031 -17.050
1DT5 C5 4 -1.811 -6.050 -16.847
1DT5 C7 5 -1.946 -6.006 -16.799
1DT5 1H7 6 -2.022 -6.073 -16.840
1DT5 2H7 7 -1.949 -6.010 -16.690
1DT5 3H7 8 -1.965 -5.904 -16.833
1DT5 C4 9 -1.713 -6.088 -16.747
1DT5 O4 10 -1.732 -6.086 -16.625
1DT5 N3 11 -1.592 -6.127 -16.799
1DT5 H3 12 -1.515 -6.156 -16.727
1DT5 C2 13 -1.558 -6.133 -16.933
1DT5 O2 14 -1.447 -6.169 -16.969
1DT5 O5' 15 -1.881 -5.889 -17.231
1DT5 C5' 16 -1.761 -5.825 -17.278
1DT5 H5'1 17 -1.716 -5.763 -17.200
1DT5 H5'2 18 -1.788 -5.762 -17.363
1DT5 C4' 19 -1.660 -5.929 -17.322
1DT5 H4' 20 -1.582 -5.886 -17.385
1DT5 O4' 21 -1.592 -5.969 -17.203
1DT5 C1' 22 -1.624 -6.101 -17.166
1DT5 H1' 23 -1.538 -6.168 -17.169
1DT5 C3' 24 -1.718 -6.058 -17.379
1DT5 H3' 25 -1.813 -6.043 -17.431
1DT5 C2' 26 -1.741 -6.142 -17.254
1DT5 H2'1 27 -1.848 -6.160 -17.241
1DT5 H2'2 28 -1.690 -6.238 -17.264
1DT5 O3' 29 -1.627 -6.124 -17.465
1DT5 HO5' 30 -1.968 -5.841 -17.239
....
24DC3 HO3' 756 -6.156 -6.186 -14.141
...
100.00000 100.00000 100.00000
The pdb file was cleaned for heteroatoms by script tough none was present initially.
I tried changing the char to unichr which created 3160 chains
there is lines like this:
2263DA N932143 -7.028 -10.568 15.373
i don't know if the columns cant be differentiated here?
what can i do to make it work?
apologies if this is trivial i am new at simulating
thanks for your help!
Best regards Chris
I ran the tutorial for the ds dna succesfully but switching over to my own structure caused an error while martinizing with python version 2.7.17:
python martinize-dna.py -dnatype ds-stiff -f origami-cleaned.gro -o cg-origami.top -x cg-origami.pdb
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 elnedyn22dna 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-dna.py", line 5070, in <module>
main(options)
File "martinize-dna.py", line 4522, 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)
The origami: origami-cleaned.gro
consist of 84 chains and looks like
162545
1DT5 N1 1 -1.656 -6.096 -17.021
1DT5 C6 2 -1.780 -6.056 -16.978
1DT5 H6 3 -1.857 -6.031 -17.050
1DT5 C5 4 -1.811 -6.050 -16.847
1DT5 C7 5 -1.946 -6.006 -16.799
1DT5 1H7 6 -2.022 -6.073 -16.840
1DT5 2H7 7 -1.949 -6.010 -16.690
1DT5 3H7 8 -1.965 -5.904 -16.833
1DT5 C4 9 -1.713 -6.088 -16.747
1DT5 O4 10 -1.732 -6.086 -16.625
1DT5 N3 11 -1.592 -6.127 -16.799
1DT5 H3 12 -1.515 -6.156 -16.727
1DT5 C2 13 -1.558 -6.133 -16.933
1DT5 O2 14 -1.447 -6.169 -16.969
1DT5 O5' 15 -1.881 -5.889 -17.231
1DT5 C5' 16 -1.761 -5.825 -17.278
1DT5 H5'1 17 -1.716 -5.763 -17.200
1DT5 H5'2 18 -1.788 -5.762 -17.363
1DT5 C4' 19 -1.660 -5.929 -17.322
1DT5 H4' 20 -1.582 -5.886 -17.385
1DT5 O4' 21 -1.592 -5.969 -17.203
1DT5 C1' 22 -1.624 -6.101 -17.166
1DT5 H1' 23 -1.538 -6.168 -17.169
1DT5 C3' 24 -1.718 -6.058 -17.379
1DT5 H3' 25 -1.813 -6.043 -17.431
1DT5 C2' 26 -1.741 -6.142 -17.254
1DT5 H2'1 27 -1.848 -6.160 -17.241
1DT5 H2'2 28 -1.690 -6.238 -17.264
1DT5 O3' 29 -1.627 -6.124 -17.465
1DT5 HO5' 30 -1.968 -5.841 -17.239
....
24DC3 HO3' 756 -6.156 -6.186 -14.141
...
100.00000 100.00000 100.00000
The pdb file was cleaned for heteroatoms by script tough none was present initially.
I tried changing the char to unichr which created 3160 chains
there is lines like this:
2263DA N932143 -7.028 -10.568 15.373
i don't know if the columns cant be differentiated here?
what can i do to make it work?
apologies if this is trivial i am new at simulating
thanks for your help!
Best regards Chris
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- Fondyffendof
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4 years 4 days ago #8498
by Fondyffendof
Replied by Fondyffendof on topic martinize-dna.py
Found the solution myself but if anyone else comes into the same problem i will rely the solution here:
The cut_off range was way to low for my system creating a huge number of chains in my case.
the reason i needed a high cut off range up to 100.0 was because of the multiple convertion of the sequence for the origami creating large bond distances.
The cut_off range was way to low for my system creating a huge number of chains in my case.
the reason i needed a high cut off range up to 100.0 was because of the multiple convertion of the sequence for the origami creating large bond distances.
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- riccardo
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4 years 4 days ago #8499
by riccardo
Replied by riccardo on topic martinize-dna.py
Thanks for posting here the solution you found!
And sorry nobody could be of help.
And sorry nobody could be of help.
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- Fondyffendof
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4 years 4 days ago #8500
by Fondyffendof
Replied by Fondyffendof on topic martinize-dna.py
No worries thanks for trying
A final note should be to make sure the correct chains are formed with correct number of residues.
If this is not the case split them off into individual gro files and combine after martinizing using cat
A final note should be to make sure the correct chains are formed with correct number of residues.
If this is not the case split them off into individual gro files and combine after martinizing using cat
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