VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Thu Jan 28 2021 - 10:45:17 CST

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