Hello,

I am trying to calculate interaction energies of ligand with a protein that I got from ACEMD simulation (I have the file has a .psf file) and I intend doing that using the below script;

from ffevaluation.ffevaluate import FFEvaluate, loadParameters, viewForces from moleculekit.molecule import Molecule from htmd.home import home from os.path import join datadir = home(dataDir='thrombin-ligand-amber') # Load the parameters prm = loadParameters(join(datadir, 'structure.prmtop')) # Load the topology mol = Molecule(join(datadir, 'structure.prmtop')) # Create a FFEvaluate object ffev = FFEvaluate(mol, prm) # Load some coordinates mol.read(join(datadir, 'structure.pdb')) # Calculate energy and forces energies, forces, atom_energies = ffev.calculate(mol.coords) # Visualize the forces viewForces(mol, forces * 0.1) # Calculate interaction energy between the protein and the ligand ffev = FFEvaluate(mol, prm, betweensets=('protein', 'resname MOL')) energies = ffev.calculateEnergies(mol.coords)

However, to do this I need my file as an amber topology file, I already tried converting using: pmd.load_file('structure.psf').save('structure.top'). But I suspect the topology derived here is in gromacs format, hence the script does not work for the .top in gromacs

I also tried converting using; pmd.amber.AmberParameterSet('srtucture.psf').save('name.prmtop') but it still didn't work, I keep getting this error of AmberParameterSet object has no attribute 'save'. Could any one suggest how I can go about this? Because I have also tried antechamber but it still doesn't work. OR I can calculate interaction energies in ACEMD?