normal Custom Mapping for an ion with Martinize2

  • mason
  • mason's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 7 months ago #9243 by mason
Hi folks,

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.

More
2 years 7 months ago #9244 by tsjerk
Replied by tsjerk on topic Custom Mapping for an ion with Martinize2
Hi Mason,

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
  • mason's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 7 months ago - 2 years 7 months ago #9247 by mason
Replied by mason on topic Custom Mapping for an ion with Martinize2
Hi Tsjerk,

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
Last edit: 2 years 7 months ago by mason. Reason: Editing this post due to bad behavior of square brackets under block quote [quote]s. Fixing so relevant bits are visible.

Please Log in or Create an account to join the conversation.

  • mason
  • mason's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 7 months ago #9263 by mason
Replied by mason on topic Custom Mapping for an ion with Martinize2
Bump

Please Log in or Create an account to join the conversation.

Time to create page: 0.102 seconds