VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Sun Nov 22 2020 - 09:12:01 CST

Dear everyone,

Thank you for your replies. I managed to get CHARMM-GUI to work for my
system and am running the Gromacs simulations for the relevant glycoprotein
now.

Thanks and Best Regards,
Manas

On Sun, Nov 22, 2020 at 11:55 AM Krishna Vkm <krishnatifr_at_gmail.com> wrote:

> 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
>>
>