On 12/06/2012 11:17 AM, flavio seixas wrote: > 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.
a = automodel(env, ...) a.toplib = 'my_top_heav.lib' a.parlib = 'my_par.lib' a.make()
> 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.
Ben Webb, Modeller Caretaker