AMBER Archive (2008)

Subject: AMBER: AMBER file preparation for protein-carbohydrate complex

From: Neha Gandhi (
Date: Thu May 22 2008 - 09:31:50 CDT

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.

Neha Gandhi

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