[gmx-users] NDG/BGLC Not Recognised In Force Fields

[McDonnell, Thomas]

Hey



Apologies for not being clearer, the NDG is from the crystal structure, the post CHARMM-GUI now outputs that residue as BGLC, however, this is also not recognised when I run gmx2pdb.



I have up to step 5 of the CHARMM-GUI, is there a way of inputting this to Gromacs without going through the GMX gmx2pdb process?



Thanks



Thomas.





On 3/17/20 12:57 PM, McDonnell, Thomas wrote:

> Hey

>

> I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is:

>

> N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2

>

> How do I modify the input files to overcome this, or is there a different forcefield I should be using?



What is NDG? There is no such residue or patch in the CHARMM force field

so I don't know why CHARMM-GUI produced any file with such a residue name.



-Justin