On Fri, Mar 26, 2021, Cato, Lee wrote:
>
>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.
Do you want to use the CHARMM force field or the Amber (GLYCAM) force fields
for this simulation?
For the CHARMM force field, the "chamber" action in ParmEd should generate
the prmtop file you need, (assuming you don't need a Drude simulation.)
For the Amber force fields, check here:
http://www.charmm-gui.org/?doc=faq
The answer to "How can I generate Amber simulation inputs using the Amber
force fields? "indicates support for GLYCAM 06 force fields. (Assuming it
works, this should be the simplest path.)
As Carlos points out, you should be able to also use the GLYCAM web site to
create a compatible PDB file. (I've used this for small problems, but never
for anything big or very complicated.)
...good luck....dac
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Received on Fri Mar 26 2021 - 14:00:02 PDT
