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Lipidated amino acids with Martinize2
- anjukris
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2 years 4 months ago - 2 years 4 months ago #9241
by anjukris
Lipidated amino acids with Martinize2 was created by anjukris
Hello,
The protein of my interest has three lipidated amino acids (CYP and CYF) and I've been trying to use martinize2 to get a Martini structure of the same.
However, the script does not recognize these amino acids in my atomistic structure file and throws warnings. How do I go about rectifying this?
I tried following the solution provided on this old thread - md.chem.rug.nl/index.php/component/kunen...no-acids-in-martini3
as well as here - www.cgmartini.nl/index.php/component/kun...lation-with-martini3
I tried to modify one of the existing map files to map these residues to Martini22 and I used the -map-dir flag as well.
However this is the error I get:
File "/home/user/.local/bin/martinize2", line 797, in <module>
entry()
File "/home/user/.local/bin/martinize2", line 557, in entry
known_force_fields)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 427, in read_mapping_directory
new_mappings = read_backmapping_file(infile, force_fields)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 111, in read_backmapping_file
weights, extra, name_to_index)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 166, in make_mapping_object
idx_to = to_name_to_idx[atname_to]
KeyError: 'SC1
Help would be greatly appreciated!
Best,
Anjali
The protein of my interest has three lipidated amino acids (CYP and CYF) and I've been trying to use martinize2 to get a Martini structure of the same.
However, the script does not recognize these amino acids in my atomistic structure file and throws warnings. How do I go about rectifying this?
I tried following the solution provided on this old thread - md.chem.rug.nl/index.php/component/kunen...no-acids-in-martini3
as well as here - www.cgmartini.nl/index.php/component/kun...lation-with-martini3
I tried to modify one of the existing map files to map these residues to Martini22 and I used the -map-dir flag as well.
However this is the error I get:
File "/home/user/.local/bin/martinize2", line 797, in <module>
entry()
File "/home/user/.local/bin/martinize2", line 557, in entry
known_force_fields)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 427, in read_mapping_directory
new_mappings = read_backmapping_file(infile, force_fields)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 111, in read_backmapping_file
weights, extra, name_to_index)
File "/home/user/.local/lib/python3.6/site-packages/vermouth/map_input.py", line 166, in make_mapping_object
idx_to = to_name_to_idx[atname_to]
KeyError: 'SC1
Help would be greatly appreciated!
Best,
Anjali
Last edit: 2 years 4 months ago by anjukris.
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