VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Wed Jan 27 2021 - 17:46:11 CST

Thanks all. It seems using the newest molfracture with vmd1.9.4 removes the
error and the peptide bonds are preseved.

That said, I still cannot get an STR file since the cgenff server complains
about both the whole protein or the single modified residue so I still
cannot get fftk to start optimizing the structure. Does vmd have any other
way I can create an str file for fftk besides the cgenff server?

Thanks!
Eddie
BTW, when the residue is submitted alone it complains "...attype warning:
carbon radical, carbocation or carbanion not supported;skipped molecule.
....." and charmmgui asks for a topology and parameter file for the
residue so that's no help.

On Wed, Jan 27, 2021 at 12:01 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> 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
>
> topology blah.top
>
> segment S {
>
> residue 1 XXX
>
> }
>
> #add some initial coordinates here from the pdb you get out of molefacture
>
>
>
> regenerate angles dihedrals
>
> guesscoord
>
> writepsf tmp.psf
>
>
>
> -Josh
>
>
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of "Prof. Eddie" <
> eackad_at_siue.edu>
> *Reply-To: *"eackad_at_siue.edu" <eackad_at_siue.edu>
> *Date: *Wednesday, January 27, 2021 at 10:15 AM
> *To: *Vmd l <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: novel residue creation and parameterization
>
>
>
> 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
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!r5H2yZmtWQ9e6mGhBDKQu7hZXAgCA_K1dTnEeTEam2sgLCFLCqof0f9csgsq_PLE0w$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390