AMBER Archive (2008)

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

From: Lachele Foley (Lists) (
Date: Thu May 22 2008 - 16:39:44 CDT

Tell me if I understand you. You want to assign charges to the
carbohydrate, but you want to use different charges from those
provided by GLYCAM. Is that right? If so, it might be simplest to
make a separate set of prep files by copying over the relevant GLYCAM
residues and changing the charges in the new file(s).

However, it is not generally recommended that you alter the GLYCAM
charge set. Why not use the charges from GLYCAM? Also, is your pdb
file being generated using GLYCAM residues, or was it generated

There is discussion of a similar issue in the AmberTools manual, by
the way (page 61, section If you have not already, you
might find it useful to read through that.

On Thu, May 22, 2008 at 10:31 AM, Neha Gandhi <> wrote:
> 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

:-) Lachele
Lachele Foley
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