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#1

Hi everyone,

I am trying to read a pdb file that  has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads: # I think right now that Mini has to have at least three atoms per residue, # hence the virtual atoms. NAME CL IO_STRING CL Z TYPE LIGAND PROPERTIES CHARGED AA UNK ROTAMERS BASIC ATOM CL Cl1p Cl1p -1.00 ATOM V1 VIRT VIRT 0.00 ATOM V2 VIRT VIRT 0.00 BOND CL V1 BOND CL V2 BOND V1 V2 CHARGE CL FORMAL -1 NBR_ATOM CL NBR_RADIUS 0.01 ICOOR_INTERNAL CL 0.000000 0.000000 0.000000 CL V1 V2 ICOOR_INTERNAL V1 0.000000 180.000000 1.493765 CL V1 V2 ICOOR_INTERNAL V2 0.000000 62.060678 1.415324 V1 CL V2 When I include this file to read the chloride residue with rosetta, the following error is thrown: ERROR: unrecognized mm_atom_type_name Cl1p ERROR:: Exit from: src/core/chemical/MMAtomTypeSet.hh line: 85 The MM atom type named Cl1p cannot be found in the files at$ROSETTA_HOME/main/database/chemical/mm_atom_type_sets/fa_standard directory. However an entry for atom type CL is found in the file mm_atom_properties.txt. So I did replace the name Cl1p with CL in the params file and a new error emerged:

ERROR: unrecognized atom_type_name 'CL'
ERROR:: Exit from: src/core/chemical/AtomTypeSet.cc line: 176

Again looking the file \$ROSETTA_HOME/main/database/chemical/atom_type_sets/fa_standard/atom_properties.txt I found tha there is a line for a chloride with name Cl. Changing the atom type CL for Cl in the params file and running again Rosetta to read the structure is now successfull. The params file now reads:

# I think right now that Mini has to have at least three atoms per residue,
# hence the virtual atoms.
NAME CL
IO_STRING  CL Z
TYPE LIGAND
PROPERTIES CHARGED
AA UNK
ROTAMERS BASIC
ATOM CL   Cl  CL   -1.00
ATOM  V1  VIRT  VIRT    0.00
ATOM  V2  VIRT  VIRT    0.00
BOND CL    V1
BOND CL    V2
BOND  V1   V2
CHARGE CL FORMAL -1
NBR_ATOM CL
ICOOR_INTERNAL   CL      0.000000    0.000000    0.000000  CL     V1    V2
ICOOR_INTERNAL    V1     0.000000  180.000000    1.493765  CL     V1    V2
ICOOR_INTERNAL    V2     0.000000   62.060678    1.415324   V1   CL     V2

Even though the file is processed I am now wondering if the parameters used are reasonably valid to continue with the simulations. Also, I am not sure whom created this CL.params file and which atom types he/she had in mind, which I could not find in the database.  Has anyone encountered with this kind of situation trying to modelling chloride anions with Rosetta?

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Mon, 2018-08-27 14:29
Martin Floor

Chloride was recently added twice by two different people.  I'm pinging them both.

The scorefunction is never particularly trustworthy on details for stuff like ligands - so given that "it's only but so good", feel confident that the changes you made locally to get it working were the right ones!

Mon, 2018-08-27 14:50
smlewis

That's what I wanted to hear!

Anyway, it would be nice to have some comments about how the parameters were achieved for the CL.params file, given that it is still orphan because the missing atom type parameters.

I will put this as solved, but feel free (y'all) to comment for future references.