I recall the GLYCAM team recently saying that they had developed tools that
could use coordinates to assign all of the required glycan names and
parameters, and not rely on the PDB residue names being correct for Amber.
You might contact them directly if they don't reply here.
On Fri, Mar 26, 2021 at 12:35 PM Cato, Lee <michael.lee.cato.emory.edu>
wrote:
> Hi,
>
> I am trying to run some simulations with a glycoprotein model originally
> optimized for CHARMM. Unfortunately, do the differences in glycan
> nomenclature specifically, I am unable to generate the file for simulation
> in amber with the current pdb. The protein is quite large, so I would
> rather not have to manually convert all glycan to amber formatting.
>
> Is it possible to use CHARM or another software to make a simple
> conversion to an amber compatible pdb?
>
> Thanks
>
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Received on Fri Mar 26 2021 - 10:00:02 PDT
