VMD-L Mailing List

From: Mariano Spivak (mariano_at_ks.uiuc.edu)
Date: Thu Jan 28 2021 - 11:40:10 CST

Hi,

As Peter suggested, the problem is most likely the incomplete assignment of the bond orders in your novel residue. Therefore when you write a MOL2 file and use it in cgenff you get the error you mentioned.
The error might come because Molefacture does not assign the bond orders perfectly, however you can fix this in Molefacture using the “Bond order” button:
First load your novel residue only (either by creating it from scratch or using a selection of a pdb)
Second, even though the structure might look correct, you might have a for example a double bond not assigned as such.
One way to test this is to use the “Add hydrogens” button in Molefacture, basically any supposedly double bond would be saturated because it was not properly set as double bond.
Use the “undo” button to go back, and select the atoms you want to change the bond order and use the “Bond order” button to specify the correct bond order.

Let me know if this helps

Best

> On Jan 28, 2021, at 10:45 AM, 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 <mailto: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 <mailto: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 <mailto: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 <mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of "Prof. Eddie" <eackad_at_siue.edu <mailto:eackad_at_siue.edu>>
> Reply-To: "eackad_at_siue.edu <mailto:eackad_at_siue.edu>" <eackad_at_siue.edu <mailto:eackad_at_siue.edu>>
> Date: Wednesday, January 27, 2021 at 10:15 AM
> To: Vmd l <vmd-l_at_ks.uiuc.edu <mailto: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