- Posts: 9
Custom Mapping for an ion with Martinize2
- mason
- Topic Author
- Offline
- Fresh Boarder
I have used the Martinize2 script to map a protein from Charmm36 to Martini3, and that worked out well. However the pdb structure of my protein includes a calcium ion I would like to include in my structure, and that is where I am having trouble.
What I am trying to do is A) define a mapping for the ion and B) rely on the ions.itp shipped with Martini3, using the CA bead type in that force field.
I have tried the following command, and some permutations, with no luck:
martinize2 -f ../protein.gro -x ./protein.pdb -o ./topol_cg.top -ff martini3001 -from universal -map-dir /path/to/mapdir -ff-dir /path/to/martini_v300 -p backbone -ignh -ignore HOH
My mapping file is called calcium.ion.map and looks like this:
[ molecule ]
CA
[from]
universal
[to]
martini3001
[ martini ]
CA
[ mapping ]
charmm36
[ atoms ]
1 CAL CA
And this is relevant piece of output (note -v option doesn't seem to add any detail at this step):
WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. [ '4635-CAL401:CAL' ]
Any direction would be much appreciate. Thanks!
Mason
Please Log in or Create an account to join the conversation.
- tsjerk
- Offline
- Expert Boarder
- Posts: 103
There seems to be a bit of a mixup with the element. The mapping file looks good. Can you send the complete output of martinize?
Cheers,
Tsjerk
Please Log in or Create an account to join the conversation.
- mason
- Topic Author
- Offline
- Fresh Boarder
- Posts: 9
First, here's the line from the source .gro file (using gro as input rather than pdb for convenience):
321CAL CAL 4635 3.222 3.507 4.626
Full Martinize2 output is as follows. Note that I did run this again with -vv just to make sure, and indeed there is no additional detail about this atom. Note also I have added some more NA ions for which I have not yet created a mapping:
INFO - step - Guessing the bonds.
WARNING - unknown-residue - Can't add bonds based on atom names for residue -NA20658 because 'Residue NA 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 -NA20659 because 'Residue NA 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 -NA20660 because 'Residue NA 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 -NA20661 because 'Residue NA is not known to force field universal'. Falling back to distance criteria.
INFO - general - 6 molecules after guessing bonds
INFO - step - Repairing the graph.
INFO - general - Applying modification N-ter to residue -ALA1
INFO - general - Applying modification C-ter to residue -VAL320
WARNING - unknown-residue - Cannot recognize residue 'NA' in molecule 2. Deleting the molecule.
WARNING - unknown-residue - Cannot recognize residue 'NA' in molecule 3. Deleting the molecule.
WARNING - unknown-residue - Cannot recognize residue 'NA' in molecule 4. Deleting the molecule.
WARNING - unknown-residue - Cannot recognize residue 'NA' in molecule 5. Deleting the molecule.
INFO - step - Dealing with modifications.
INFO - general - Identified the modifications [ 'N-ter' ] on residues [ 'ALA1', 'ALA1', 'ALA1', 'ALA1' ]
INFO - general - Identified the modifications [ 'C-ter' ] on residues [ 'VAL320', 'VAL320', 'VAL320' ]
INFO - step - Read input.
INFO - step - Creating the graph at the target resolution.
INFO - general - Applying modification mapping ('C-ter',)
INFO - general - Applying modification mapping ('N-ter',)
WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. [ '4635-CAL321:CAL' ]
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
INFO - step - Applying position restraints.
INFO - step - Writing output.
Hope this helps!
Mason
Please Log in or Create an account to join the conversation.
- mason
- Topic Author
- Offline
- Fresh Boarder
- Posts: 9
Please Log in or Create an account to join the conversation.