On 3/18/20 7:56 AM, McDonnell, Thomas wrote:
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?
Doesn't CHARMM-GUI give you a GROMACS topology?
BGLC is a valid residue in CHARMM so without the actual screen output
and error message, there's not much to suggest. The main problem is one
intrinsic to pdb2gmx - it's not good at branched polymers. You'll have
what it thinks is a discontinuous chain of protein and sugar residues,
which you might be able to link/patch via specbond.dat but that requires
a lot of work. It's very easy to set up in CHARMM (which is all
CHARMM-GUI is doing on the backend).
-Justin
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
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