Hi Ben
I successfully generate charmm force fields (parameter and topology files) using swissparam server, for the ligand that is bonded to my protein template.
Now I want to built models bonded to this ligand and also optimize them using Modeller protocol for MD and SA.
My questions are:
1) How can I make modeller reads the parameter and topology files for the ligand? Is there a command for it?
2) Or should I copy and paste the ligand topology data to top_heav.lib file?
3) If the second option is the choice, where to paste the information regarding the parameters?
4) In the alignment file, how to set the symbol for the ligand? I think if I set it as BLK "." no changes will be made. Is that right?
Best regards,
Flavio