VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Jan 27 2021 - 20:13:30 CST

Doesn't the cgenff server take mol2 files as a possible input? VMD can
write these. You'll want to make sure you have all of the bonds set
properly before saving so that that information propagates.
Best,
Peter

On Wed, Jan 27, 2021 at 7:30 PM Prof. Eddie <eackad_at_siue.edu> wrote:

> 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
>