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

[Justin Lemkul]

On 3/18/20 7:56 AM, McDonnell, Thomas wrote:
> Hey
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> 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.
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> 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?
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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

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> Thanks
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> Thomas.
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> On 3/17/20 12:57 PM, McDonnell, Thomas wrote:
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>> 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?
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> What is NDG? There is no such residue or patch in the CHARMM force field
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> so I don't know why CHARMM-GUI produced any file with such a residue name.
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> -Justin
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-- 
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Justin A. Lemkul, Ph.D.
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