VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Wed Jan 27 2021 - 08:33:12 CST

Hello,
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.
Thanks,
Eddie 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!rqOLhm10ppn4K6XaJmAUON8FQtS_yDlQidgmGuMmAFBCVpARoeLBTrTciXaj7IIQPQ$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390