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Problem generating RNA topology - bases not recognized by martinize
- sajjad.ir
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5 years 8 months ago #7775
by sajjad.ir
Problem generating RNA topology - bases not recognized by martinize was created by sajjad.ir
Hi,
Recently I tried to generate a RNA topology by martinize-nucleopeptide.py script.
I followed every step that is listed in the RNA tutorial for my RNA sequence but the final structure of the cg RNA is not match with the All Atom structure at the both end of the RNA.
As you can see in the provided image, there are two bases on the top and one in the bottom that are not coarse grained.
Image LINK
Seems strange, could you please hep me find a solution for that?
Recently I tried to generate a RNA topology by martinize-nucleopeptide.py script.
I followed every step that is listed in the RNA tutorial for my RNA sequence but the final structure of the cg RNA is not match with the All Atom structure at the both end of the RNA.
As you can see in the provided image, there are two bases on the top and one in the bottom that are not coarse grained.
Image LINK
Seems strange, could you please hep me find a solution for that?
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- sajjad.ir
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5 years 8 months ago - 5 years 8 months ago #7776
by sajjad.ir
Replied by sajjad.ir on topic Problem generating RNA topology - bases not recognized by martinize
Just one more thing, the script actually generated files"
Nucleic_A+Nucleic_B.itp (for the two large strands)
Nucleic_C.itp (for the single base in the bottom of the RNA )
it seems the script cannot recognize the sequence properly
EDIT:
I finally solved this problem.
Actually the residue name in the original RNA file was not correct for Thymine (is was T except DT in the gro file).
BUT there is another problem.
I have two file
Nucleic_A+Nucleic_B.itp
Nucleic_C.itp (for the bases C and T - at the bottom of one of the strand
Nucleic_A+Nucleic_B.itp (for the two large strands)
Nucleic_C.itp (for the single base in the bottom of the RNA )
it seems the script cannot recognize the sequence properly
EDIT:
I finally solved this problem.
Actually the residue name in the original RNA file was not correct for Thymine (is was T except DT in the gro file).
BUT there is another problem.
I have two file
Nucleic_A+Nucleic_B.itp
Nucleic_C.itp (for the bases C and T - at the bottom of one of the strand
Last edit: 5 years 8 months ago by sajjad.ir.
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- ifaustino
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5 years 8 months ago #7781
by ifaustino
Replied by ifaustino on topic Problem generating RNA topology - bases not recognized by martinize
Dear sajjad.ir,
Thanks for your messages.
When martinize-nucleotide.py generates two .itp files it usually means there is something strange in the atomistic .gro file. If you are using only standard residues, make sure all residues are named like DX (e.g. DA, DC, DG, DT).
If the problem persists, try to use the atomistic .pdb with tleap (a module in Ambertools). With this you will make sure the order and the name of the atoms is correct. If you have questions on which commands to run tleap, send me an email to This email address is being protected from spambots. You need JavaScript enabled to view it..
Hope this helps,
Ignacio
Thanks for your messages.
When martinize-nucleotide.py generates two .itp files it usually means there is something strange in the atomistic .gro file. If you are using only standard residues, make sure all residues are named like DX (e.g. DA, DC, DG, DT).
If the problem persists, try to use the atomistic .pdb with tleap (a module in Ambertools). With this you will make sure the order and the name of the atoms is correct. If you have questions on which commands to run tleap, send me an email to This email address is being protected from spambots. You need JavaScript enabled to view it..
Hope this helps,
Ignacio
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