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martinize2 does not recognize RNAs residues
- willyef
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1 year 4 months ago #9550
by willyef
martinize2 does not recognize RNAs residues was created by willyef
Hey there,
I am having problem trying to martinize2 a RNA molecule.
Here is the line and I'm using and the error I got from its execution:
$ martinize2 -f chainB.pdb -o nameB.top -x nameB_cg.pdb -dssp /usr/bin/dssp -p backbone -elastic -ef 700.0 -el 0.5 -eu 0.9 -ea 0 -ep 0 -scfix -cys auto -ff martini3001
INFO - general - Merging two molecules/chains because there is a CONECT record between atoms 1362B-G204:OP2 and 2810B-MG401:MG
INFO - general - Read 1 molecules from PDB file chainB.pdb
INFO - step - Guessing the bonds.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-U140 because 'Residue U is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-C141 because 'Residue C is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-G142 because 'Residue G is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-G143 because 'Residue G is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-C144 because 'Residue C is not known to force field universal'. Falling back to distance criteria.
...
...
...
INFO - general - 1 molecules after guessing bonds
INFO - step - Repairing the graph.
WARNING - unknown-residue - Cannot recognize residue 'U' in molecule 0. Deleting the molecule.
INFO - step - Dealing with modifications.
INFO - step - Read input.
INFO - step - Creating the graph at the target resolution.
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
INFO - step - Applying position restraints.
INFO - step - Setting the rubber bands.
INFO - step - Writing output.
Traceback (most recent call last):
File "/home/willy/.local/bin/martinize2", line 797, in <module>
entry()
File "/home/willy/.local/bin/martinize2", line 776, in entry
write_gmx_topology(system, args.top_path, defines=defines, header=header)
File "/home/willy/.local/bin/martinize2", line 167, in write_gmx_topology
raise ValueError('No molecule in the system. Nothing to write.')
ValueError: No molecule in the system. Nothing to write.
Please, can someone point me to the right direction to fix this?
Thanks in advance
W.
I am having problem trying to martinize2 a RNA molecule.
Here is the line and I'm using and the error I got from its execution:
$ martinize2 -f chainB.pdb -o nameB.top -x nameB_cg.pdb -dssp /usr/bin/dssp -p backbone -elastic -ef 700.0 -el 0.5 -eu 0.9 -ea 0 -ep 0 -scfix -cys auto -ff martini3001
INFO - general - Merging two molecules/chains because there is a CONECT record between atoms 1362B-G204:OP2 and 2810B-MG401:MG
INFO - general - Read 1 molecules from PDB file chainB.pdb
INFO - step - Guessing the bonds.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-U140 because 'Residue U is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-C141 because 'Residue C is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-G142 because 'Residue G is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-G143 because 'Residue G is not known to force field universal'. Falling back to distance criteria.
WARNING - unknown-residue - Can't add bonds based on atom names for residue B-C144 because 'Residue C is not known to force field universal'. Falling back to distance criteria.
...
...
...
INFO - general - 1 molecules after guessing bonds
INFO - step - Repairing the graph.
WARNING - unknown-residue - Cannot recognize residue 'U' in molecule 0. Deleting the molecule.
INFO - step - Dealing with modifications.
INFO - step - Read input.
INFO - step - Creating the graph at the target resolution.
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
INFO - step - Applying position restraints.
INFO - step - Setting the rubber bands.
INFO - step - Writing output.
Traceback (most recent call last):
File "/home/willy/.local/bin/martinize2", line 797, in <module>
entry()
File "/home/willy/.local/bin/martinize2", line 776, in entry
write_gmx_topology(system, args.top_path, defines=defines, header=header)
File "/home/willy/.local/bin/martinize2", line 167, in write_gmx_topology
raise ValueError('No molecule in the system. Nothing to write.')
ValueError: No molecule in the system. Nothing to write.
Please, can someone point me to the right direction to fix this?
Thanks in advance
W.
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- fgrunewald
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1 year 4 months ago #9551
by fgrunewald
Replied by fgrunewald on topic martinize2 does not recognize RNAs residues
Hi,
RNA parameters are not yet available for Martini v3.0. I'd estimate a first set of parameters to become available springs next year.
Cheers,
Fabian
RNA parameters are not yet available for Martini v3.0. I'd estimate a first set of parameters to become available springs next year.
Cheers,
Fabian
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