AMBER Archive (2009)

Subject: Re: [AMBER] how to use GLYCAM04 for carbonhydrate in amber9?

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Mon Nov 30 2009 - 02:53:27 CST

Hi,

        Most of your questions can be answered by reading the AMBER documentation
(e.g. AMBER9, AMBER10, or AmberTools manuals).

        The resp charges have already been computed for most carbohydrate residues.
You can see the partial atomic charges in the file
$AMBERHOME/dat/leap/prep/glycam04.in.

        You can combine Glycam04 with other force fields, which you will need to
specify in your leap input file. When you are using an amber protein force
field, it is recommended that you use the default scaling factors (i.e. SCEE
and SCNB) for proteins.

        There is an example of how to build a polysaccharides in the AMBER9 manual,
if you do not have an input pdb structure. If you have a pdb file, then it
becomes easier - but make sure you have the residue name changed to reflect
the Glycam04 nomenclature, and the atom names assigned appropriately. You can
also go http://glycam.ccrc.uga.edu/ and build a structure via the Biomolecule
Builder pulldown menu. At this web site you can also download the latest set
of prep and parameter files.

        Essentially, you can build your carbohydrate model just as you would for a
protein model. If you are unfamiliar with the process for building a protein
model, then I suggest you look at some of the tutorials.

        Hope that helps.

Cheers,
Karl

On Monday 30 November 2009 04:39, sculiujl wrote:
> Hi amber users,
> I want to study the interactions between the carbonhydrate and the
> protein.As you know there is GLYCAM04 carbonhydate force field in amber9.
> But as a green hand in the present I donot know how to use the GLYCAM04 to
> build the carbonhydate model.

> And for the carbonhydate part whether should I calculate the resp charge
> alone or it has included in the GLYCAM04. At the same time how to combine
> GLYCAM04 with other force field which I will choose to deal with the
> protein. Thank you in advance.

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