From: Vermaas, Josh (
Date: Wed Jan 27 2021 - 12:01:29 CST

Hi Eddie,

I’m betting that the topology is missing the peptide bonds in the bond, improper, and cmap declarations in the topology file. If you look at a standard protein topology file, you’ll see entries like: “BOND C +N”, which tells psfgen about the bond between the C atom and the N atom for the next residue. Similar entries typically exist for impropers and CMAP terms, and molefacture won’t make them by default.

Does a simple psfgen script work?

package require psfgen
segment S {
residue 1 XXX
#add some initial coordinates here from the pdb you get out of molefacture

regenerate angles dihedrals
writepsf tmp.psf


From: <> on behalf of "Prof. Eddie" <>
Reply-To: "" <>
Date: Wednesday, January 27, 2021 at 10:15 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