Hello Sir,
I am trying to run MD for a docked complex, the ligand is pretty big
which contains a hydroxymethylconduritol unit and a
4-amino-4-deoxy-D-chinovose residue linked to number (8-12) of
a-D-glucose units.
i was able to run antechamber for some small molecules successfully, but
i struck with this molecule.
please give me a brief idea to break and build the molecule or otherwise
how to incorporate glycam force field in to Amber or any other way to go
about it.
Thanking you.
On 2014-01-15 22:15, David A Case wrote:
> On Wed, Jan 15, 2014, Arun Kumar Somavarapu wrote:
>
>> In your earlier message you suggested me to break the molecule, as i am new to Amber may be i will generate files for individual piece but i have no idea about next steps (like how to link and proceed).
>
> Linking sugars together to form poly-saccharides is a bit of a specialized
> task. Go to the online glycoprotein builder:
>
> http://glycam.ccrc.uga.edu/ccrc/gp/ [1]
>
> and see if that will do what you want. Detailed questions posted there (or
> here) usually get answered pretty quickly. But you will have to give details
> about your chemistry: just saying that what you have is "similar to glucose"
> is not enough. If the web site above doesn't help (enough), post *exactly*
> what you tried and the what the problem was.
>
> ...dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [2]
--
Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
Links:
------
[1] http://glycam.ccrc.uga.edu/ccrc/gp/
[2] http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jan 15 2014 - 23:30:02 PST
