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SPICA-group / spica-tools

Tools for coarse-grained molecular dynamics simulations using the SPICA force field
https://spica-group.github.io/spica-tools/
MIT License
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ERROR: ILE ATOM ['CB', 'CD', 'CG1', 'CG2'] IS MISSING ON MOLECULE #25

Closed alphataubio closed 5 months ago

alphataubio commented 8 months ago

cg_spica map2cg -verbose 1 2q3z.pdb 2q3z.cg.pdb

ERROR: ILE ATOM ['CB', 'CD', 'CG1', 'CG2'] IS MISSING ON MOLECULE 112

https://files.rcsb.org/download/2Q3Z.pdb

yskmiyazaki commented 8 months ago

@alphataubio The mapping list for ILE (src/map_to_cg.py , line 135) does not include "CD1" in 2q3z.pdb. Both atomic names "CD1" and "CD" can be used on PDB though. For the error

We intend to update the code to allow for this slight difference in atomic names.

However, there is a residue in 2q3z.pdb called "ONL" (5-oxo-L-norleucine) that has not ever been parameterized in SPICA. Therefore, to complete the mapping, you need to add a mapping for "ONL" in the code ( and assign a parameter for simulations).

alphataubio commented 5 months ago

thanks i ran the pdb file thru charmmgui to clean it up, then spica-tools to generate LAMMPS inputs.

https://youtu.be/rZ1wmy-RDpw