VMD-L Mailing List

From: Krishna Vkm (krishnatifr_at_gmail.com)
Date: Sun Nov 22 2020 - 05:55:05 CST

Hi Manas
I have simulated the RBD domain of SPIKE protein which is glycosylated. For
this protein, I tried to generate the PDB and PSF file in vmd but it was
nightmare for me. So, I took the help of charmmgui server and able to
create psf and pdb file successfully.

Regards
Krishna

On Sat, Nov 21, 2020 at 2:17 AM Manas Kohli <manaskohli1_at_gmail.com> wrote:

> Dear All,
>
> I'm wondering if anyone has performed a simulation on Glycoproteins with
> either NAMD or Gromacs. Specifically I'm trying to find a way to go about
> doing this, what force-field and parameter files do people use since I'm a
> bit confused/lost. I'm currently trying to simulate a membrane protein
> covalently bonded to a sugar tree docked to another extracellular protein.
> To summarize the steps I've undertaken:
>
> 1. I used the GLYCAM server to build the appropriate glycoprotein. From
> what I've seen, the server uses its own format to build the sugar tree. So
> for example, a NAG residue could be named 4YB. Atom Names are also
> correspondingly different between the two - for example, there is a C8
> atomname in typical NAG residues but C2N in 4YB.
>
> 2. I then changed the name of the residues back to apparently a more
> standard PDB glycan residue name that could be recognized by the
> protein-protein docking software HADDOCK. I changed 4YB for instance back
> to NAG.
>
> 3. HADDOCK recognized the sugar residues but changed the atom naming from
> the GLYCAM convention to their own. The sugar tree though was maintained
> during the docking run and the protein seems to have docked in a good
> conformation/one that I expect.
>
> 4. I then tried to build a corresponding topology for the glycoprotein.
> For the glycan residues, I tried to use tleap from Amber-tools with GLYCAM
> force-fields to build a topology in AMBER for the sugar residues. Then
> there is another program to convert an AMBER topology to a GROMACS topology
> which I planned to use in Gromacs. However, with the change in residue
> naming and atom naming, this is where I'm stuck.
>
> So I had two major questions from this
>
> 1) How exactly do I convert between a GLYCAM and PDB format to have an
> appropriate naming for residues and atoms for both HADDOCK and then
> correspondingly Amber-Tools
>
> 2) When I create a topology using the glycam force-field for the sugar
> residues, how do I ensure I'm able to capture the covalent bond between the
> Asn residue of my glycoprotein and the rest of the sugar tree.
>
> I may be doing something completely wrong with this but I'm very confused.
> If anyone has had experience in simulating glycoproteins, I'd appreciate
> it! I don't personally mind mapping the atom names back from the PDB format
> HADDOCK recognizes to the GLYCAM format but I had the major question as to
> how to maintain a covalent bond between the protein and sugar trees in my
> topology file if I were to isolate the glycans to use this with the GLYCAM
> force-field.
>
> Thanks and Best Regards,
> Manas
>