AMBER Archive (2008)

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

Date: Sun May 25 2008 - 02:17:55 CDT

Thank you very much for posting your reply. You are right but the
issue is the pdb is a heparin fragment which has sulfated IdoA and

Building AMBER input files with carbohydrates is easy and it can done
through glycam website. But I am working with gags. I assigned glycam
atom type and residue to it and sulfate parameters from Altona's paper
but glycam residue type doesnot have sulfates included in it. Hence,
AMBER cannot identify the atom type or residue name for my molecule
which has sulfates.

For example you can extract heparin from 2HYU file and try to prepare
input files for AMBER.
How do I prepare pdb file for this sulfated molecules? I have
obviously calculated RESP charges.


On 5/23/08, Lachele Foley (Lists) <> wrote:
> 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
> elsewhere?
> 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
>> 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
> 2-0263
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to

Neha Gandhi
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)