I successfully generate charmm force fields (parameter and topology
files) using swissparam server, for the ligand that is bonded to my
protein template.
In most cases it's easier just to use a BLK residue for ligands.
Modeller will take care of the protein-ligand interactions
automatically. If you define parameters for the ligand yourself, you'll
probably have to take care of interactions between the protein and the
ligand yourself. Note also that since the default Modeller forcefield
does not include an electrostatic term, any charged interactions will
probably be incorrect.
1) How can I make modeller reads the parameter and topology files for
the ligand? Is there a command for it?
You have to put all the parameters in one file, and all the topology in
another - you can't read multiple parameter files. You can either do
this by modifying the top_heav.lib and par.lib files that ship with
Modeller, or copy them and modify the copies. If you do the latter,
you'll need to set toplib and parlib in the automodel class to point to
them, e.g.
3) If the second option is the choice, where to paste the information
regarding the parameters?
For the residue topology, just add it to the end of the file - Modeller
doesn't care about the order (if you defined new atom types though,
you'll have to add them at the start of the file with the existing
types). For the parameters, CHARMM format has separate sections for each
type of parameter - you'll have to add your parameters to the right
sections.
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?
You'll need to use whichever one-letter code you chose in restyp.lib.
See the FAQ.