VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Thu Jan 28 2021 - 15:22:59 CST

Thank you! That worked to get it into cgenff. I guess I'll just use fftk to
optimized the parameters for this "terminated" residue and then remove the
backbone part.
Thanks all!

On Thu, Jan 28, 2021 at 2:36 PM Smith, Harper E. <
smith.12510_at_buckeyemail.osu.edu> wrote:

> Hi Eddie,
>
> There are N/C terminal patches you can apply to your residue. One idea
> might be to acetylate the N-terminus (patch ACE) and methylamidate the
> C-terminus (patch CT3).
>
> HTH,
> Harper
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Prof. Eddie <eackad_at_siue.edu>
> *Sent:* Thursday, January 28, 2021 3:21 PM
> *To:* Peter Freddolino <petefred_at_umich.edu>
> *Cc:* Vmd l <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: novel residue creation and parameterization
>
> The novel residue attaches to the carbon alpha of the backbone just as any
> sidechain so there is nothing funky there. But if I make a fragment of just
> the sidechain to save then some bonds need to get left out and so this is
> what causes the problem. If I include the backbone I have "dangling" bonds
> there. If I try just the sidechain I have a dangling bond there. I don't
> see how without inputting the complete protein I can avoid that, but I
> can't see how using the whole protein is reasonable either. How can I give
> cgenff something that doesn't have a dangling bond then? Do I have to
> treat it as a ligand and add hydrogens to terminate say the backbone atoms
> and then manually remove those from the topology file?
> Thanks again for your help!
> Eddie
>
> On Thu, Jan 28, 2021 at 12:24 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
> Hi Eddie,
> You certainly shouldn't be parameterizing the whole protein, only the new
> residue that you're trying to add. What is the chemistry of the attachment
> of your new component to the rest of the protein? Is it incorporated to the
> protein backbone in some way, or is it a modification attached to a side
> chain? The protein topologies are by design pretty modular, so what you
> just need to figure out is what is an appropriate attachment point beyond
> which you can treat your new component like any other part of the protein
> force field. Just for example, if you were trying to add a new amino acid,
> you would likely assume (unless the beta carbon had some really funky
> chemistry) that you can use the same backbone parameters as all other amino
> acids in the charmm forcefield, and then focus on parameterizing your
> fragment and its attachment to the alpha carbon.
> Best, Peter
>
>
> On Thu, Jan 28, 2021 at 12:32 PM Prof. Eddie <eackad_at_siue.edu> wrote:
>
> Hello,
> I'm not sure how to do that. Molfracture saves each residue in its own
> mol2 file. Otherwise, I need to rename the whole protein to have 1 residue
> name. Even then cgenff says I have a carbene and won't proceed (although
> molfracture does not find anything which a large charge). Is there some
> other way to write it?
>
> Also, do I need the whole protein put into cgenff or is there a way to
> just have my novel residue and have it ignore the (incomplete) backbone? I
> would just like to get the files so I can use fftk (which may also be
> difficult if I need the whole protein in gaussian instead of just the novel
> residue).
> Thanks,
> Eddie
>
>
> On Wed, Jan 27, 2021 at 8:13 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
> 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
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!sSBpn5YJnqidDOYbRGzktV95oW_ghLXFz7nutMjE95Y7BYt1mAvDxV9wpRCbQKiEEw$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!vgXwHoaPNb-mbp8Jn-Kuh1Y3IMgXAk5xKbGZnXx5wP7wnK6frjiWNWKdoI74XHheyg$>
> 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!pRQ21qDFHiBfacPd9erMf3TZEXoU-juJI4tN_IPQsy_RS02jDOMbewLSkzd-Ew6c3w$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390