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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
