Hi All,
I am working on protein-charged carbohydrate complex and I want to perform
MD simulations. The ligand has charged groups. PDB file format allows easy
assignment of charges for the protein based on 3 letter amino acid code but
how this format is not useful for charged ligands. I am using RESP charged
and GLYCAM forcefield for the carbohydrate.
Mol2 file format is also not helpful as it ll work for only a single residue
in AMBER. How I prepare the input file for ligand-receptor complex for AMBER
in this case?
Again, the other issue will be the amino acid name will be truncated in case
of ligand when I run ambpdb. In this case, the carbohydrate residue has
nomenclature based on glycam.
Your help is appreciated.
--
Regards,
Neha Gandhi
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Received on Sun May 25 2008 - 06:07:30 PDT
