I am using CHARMM-GUI to generate the files for MDS for protein-ligand complex and I noticed that the partial charges generated from the webserver for the ligand in .rtf file are different from the ones generated from openbabel (gasteiger charges).
Should I modify the charges in the file generated by CHARMM-GUI to be the same as the ones from openbabel?
Stéphane Abel Thank you for your explanation. Yes, sometimes I see large penalties. What should I do?
Stéphane Abel so you mean to refine the charges and modify the .rtf file of the ligand, right? but if i do that how can i get the penalties? because if i refined the ligand then uploaded it again to CHARMM-GUI in .mol2 format to get the penalties, the website will change the charges again. or do the QM programs produce some kind of a score to know the quality of the charges?
also, could you suggest some free QM programs to refine the structure?
this is the line that shows the penalties:
RESI UNK 0.000 ! param penalty= 66.000 ; charge penalty= 23.509
by bonded parameters you mean the param penalty, right?
Thanks for your help
Stéphane Abel thank you for your help and suggestions of programs. For the refinement of dihedrals, should I refine the dihedral angles of the ligand after it has been docked to the protein? is not this going to change the docked pose?
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