Hello.
I am trying to parametrize a ligand using SwissParam. It generated me topology (.rtf) and parameter (.prm) files, but the topology file isn't working in Autopsf so I can't generate a .psf file for my future NAMD simulation.
Below is the topology file, mol2, and the prm. My assumption is that the ligand has atoms not supported by the CHARMM force field.
Aarav Singh It's because the resname is not defined in the mol2 file.
save it into a pdb file with the resname as defined in the topology file (it's QE2 here) then you can be able to get the psf from VMD.
I've attached the pdb for your reference.
Thank you Dinesh!
My procedure now is loading the protein and ligand separately into VMD ( protein by pdb and ligand my mol2). Build separate psfs. Then I added the two psfs together with the read command readpsf (ligand.psf) and readpsf (ligand.psf). Then I do writepsf (combined.psf). This is done in VMD TkConsole
This creates a psf for both the protein and ligand. The pdb I just used texteditor and manually added the ligand pdb to the protein pdb and made sure it aligned with the combined psf requirements.
But yes the issue was solved by using texteditor to make sure everything aligned essentially.
I hope this helps anyone using swissparam in protein-ligand NAMD simulations!