Molecular Systems

The topology of my molecular system is not recognized by AquaLab.

When a msystem is initialized with a pdb or gro file, the topology -covalent bonds- and the properties of atoms are taken from the data stored in the directory Aqua/top_par. These pre-defined topologies have been implemented according to the residue and atom names found in the most popular water and protein models included in GROMACS, CHARMM or NAMD.

If your system is not described by AquaLab there are three ways to proceed:

1. Create your own psf file to initialize the msystem. If the psf file does not include a list of donors and acceptors, they have to be set up with msystem.add_donors() and msystem.add_acceptors().
2. Find a template to create a new topology in Aqua/top_par/top_par_template.py. Include an edited copy with the description of your molecular system in the directory Aqua/top_par. And add to the file Aqua/top_par/top_par.py the line: “user_topol.append(‘your_top_par_file_name’)”. It is time now to run your script calling msystem.
3. Find a template to create a new topology in the file Aqua/top_par/top_par_template.py. Include in your working directory an edited copy with the description of your molecular system. Run your script loading the new topology with add_user_topol() before initializing the msystem.