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martinizing / dssp
- rguixa
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11 years 7 months ago #1134
by rguixa
martinizing / dssp was created by rguixa
Hi all,
I am trying to martinize a protein structure from a PDB file but the coarse-grained structure always happen to lack the last two residues. Is there anything I can do to make any of the two applications recognize these two residues? They belong to the very last part of this transmembrane protein, the intracellular C-terminal, but for some reason the files generated (both structure and topology files) do not include them. If I use verbose upon martinizing I see though the script initially recognize all residues (262):
INFO Found 1 chains:
INFO 1: X (Protein), 2097 atoms in 262 residues.
You can see no errors in the martinize output and, in addition, the aa sequence output by the script at the end seems to include them:
DEBUG 'HIS', 'CYS'[/b]]
However, both .pdb and .itp files include only 260 residues and no trace of these last HIS and CYS residues.
I have already tried using both a separate DSSP file (-ss option) and using the DSSP executable on the fly (-dssp option) but they both yield the same thing...
Any ideas??
Regards,
Ramon
I am trying to martinize a protein structure from a PDB file but the coarse-grained structure always happen to lack the last two residues. Is there anything I can do to make any of the two applications recognize these two residues? They belong to the very last part of this transmembrane protein, the intracellular C-terminal, but for some reason the files generated (both structure and topology files) do not include them. If I use verbose upon martinizing I see though the script initially recognize all residues (262):
INFO Found 1 chains:
INFO 1: X (Protein), 2097 atoms in 262 residues.
You can see no errors in the martinize output and, in addition, the aa sequence output by the script at the end seems to include them:
DEBUG 'HIS', 'CYS'[/b]]
However, both .pdb and .itp files include only 260 residues and no trace of these last HIS and CYS residues.
I have already tried using both a separate DSSP file (-ss option) and using the DSSP executable on the fly (-dssp option) but they both yield the same thing...
Any ideas??
Regards,
Ramon
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- rguixa
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11 years 7 months ago #1135
by rguixa
Replied by rguixa on topic martinizing / dssp
Hi again,
I found where the problem was. I just realized I was using non-standard naming scheme for certain atoms in my input pdb file. As you recommend in other threads, carefully checking you have the proper structure file beforehand is a must...
Sorry!
Ramon
I found where the problem was. I just realized I was using non-standard naming scheme for certain atoms in my input pdb file. As you recommend in other threads, carefully checking you have the proper structure file beforehand is a must...
Sorry!
Ramon
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- xavier
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11 years 7 months ago #1138
by xavier
Replied by xavier on topic martinizing / dssp
Good you found the solution. It is indeed good to check the input, it is nost often where the problem is :))
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