From: Smith, Harper E. (
Date: Wed Jan 27 2021 - 11:42:22 CST

Hi Eddie,

When you make your compound in Molefacture, do you write the PSF/PDB files (under File)? You might see your bond if you load the PSF along with your PDB. I recommend following the FFTK tutorial .

I needed to modify some residues in my protein, so I made a patch for AutoPSF. Then you can just apply the patch to your residue to modify it.

From: <> on behalf of Prof. Eddie <>
Sent: Wednesday, January 27, 2021 9:33 AM
To: Vmd l <>
Subject: vmd-l: novel residue creation and parameterization

I have a protein and I'd like to mutate one of the residues to a large novel compound (a progesterone analog). I need the new residue to be bonded to the backbone. I think I have two issues.
1) I was able to create the new residue using molfracture. But once I exited and applied it to the larger structure it removed the peptide bond to the neighboring residue. I had to load the whole protein into molfracture to recreate the peptide bonds with the neighboring residues. However, I just gave the default atom types and did not run any of molfractures tools so the structure is not optimized.
2) I think I need to use fftk to now parameterize the residue but to create a psf I get failures of psfgen since it says my residue type (named XXX) is unknown. I thought that would invoke the paratools screen so I'd at least have the psf to start fftk. How can I get the psf?

I appreciate any help. Most of the tutorials I've found have been for ligands (not bonded) or are direct edits to the parameter file since the novel structure is a small change. I'd like to do this more than once and so I'd like to know how to do it well.

Edward Ackad, Ph.D<*7Eeackad__;JQ!!DZ3fjg!rqOLhm10ppn4K6XaJmAUON8FQtS_yDlQidgmGuMmAFBCVpARoeLBTrTciXaj7IIQPQ$>
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390