I built PFBS (F3C-(CF2)3-SO3H) and deprotonated PFBS ([F3C-(CF2)3-SO3]-) molecular models in Material Studio and exported as PDB files, trying to obtain the OPLS-AA parameters for them using LigParGen.
Default options were used for PFBS (F3C-(CF2)3-SO3H).
molecular charge was set to -1 for deprotonated PFBS ([F3C-(CF2)3-SO3]-).
Actual Behavior
OPLS-AA parameters was successfully generated for PFBS, but got error for deprotonated PFBS ([F3C-(CF2)3-SO3]-).
I set molecular charge to -1, but still got the error message Found residue ligand MOL
I don't know whether the force field parameters and atom charges are the same between PFBS and deprotonated PFBS.
Issue Information
Software name & Version : LigParGen online Generator at http://zarbi.chem.yale.edu/ligpargen/ Method: PDB input files generated by Material Studio
Expected Behavior
I built PFBS (F3C-(CF2)3-SO3H) and deprotonated PFBS ([F3C-(CF2)3-SO3]-) molecular models in Material Studio and exported as PDB files, trying to obtain the OPLS-AA parameters for them using LigParGen. Default options were used for PFBS (F3C-(CF2)3-SO3H). molecular charge was set to -1 for deprotonated PFBS ([F3C-(CF2)3-SO3]-).
Actual Behavior
OPLS-AA parameters was successfully generated for PFBS, but got error for deprotonated PFBS ([F3C-(CF2)3-SO3]-). I set molecular charge to -1, but still got the error message Found residue ligand MOL
I don't know whether the force field parameters and atom charges are the same between PFBS and deprotonated PFBS.
Here is my PDB files, PFBS.pdb.txt PFBS_H.pdb.txt
Thank you so much in advance~