From: Hélder Bandarra Tavares (
Date: Tue May 26 2020 - 08:47:56 CDT

I'm trying to bind a molecule (mostly composed of PEG chains) to Hemolysin. I have the .pdb and .psf files of both. To do so, I placed the molecule close to the residue I want to link it to and created a bond using Molefacture, and now I wanted to generate a .psf file to run a MD minimization/equilibration afterwards with NAMD. However, using Autopsf I get the following message: "Autopsf has detected 1 unparametrized components", and this component is the molecule I want to link. It is worth noting that that molecule has no non-standard atoms and that I loaded the topology files provided by CHARMM-GUI for this molecule.

What can I do to generate the .psf file? Is there other way to do so?

Thank you in advance,

Hélder Tavares