Hi,
I was able to get prepareforleap to recognize IDU and UAP by adding
the following to the 'Carbohydrate_PDB_Glycam_Names.txt' file in
$CPPTRAJHOME/dat:
IDU U B L P "2-O-sulfo-beta-L-altropyranuronic acid"
UAP U A L P "4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid"
Unfortunately as far as I can tell GLYCAM doesn't seem to have a
residue with the N-sulfamino framework for the SGN residue (there are
only N-acetyl varieties like NAG, MGC, etc). Maybe one of the Glycam
folks can chime in and let me know if I've missed something.
If the stock Glycam FF doesn't have what you need, other people may
have generated the parameters you need. A brief search turned up this
publication which seemed promising (but full disclosure I did not read
the whole thing): https://cdnsciencepub.com/doi/10.1139/cjc-2015-0606
I'll keep trying to think about this but I'm not sure how much more
I'll be able to help. Other (smarter) people may want to step in here.
-Dan
PS - You could also try alternatives like CHARMM-GUI to model your glycoprotein.
On Fri, Mar 22, 2024 at 6:47 AM SUBHASMITA MAHAPATRA MAHAPATRA via
AMBER <amber.ambermd.org> wrote:
>
> Hello,
>
> I want to simulate this PDB:1FQ9. It has two chains of heparan sulfate
> (E,F). They have this residue 'UAP' and I am unable to find its name as per
> Glycam force field. I have tried the Glycam-web interface.
>
> Kindly help me in this regard.
>
> Thank you
>
> --
> *Yours Sincerely*
> *Subhasmita Mahapatra*
> *Ph.D. Scholar (PMRF)*
> *Computational Biophysics Group*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *Madhya Pradesh, India (453552)*
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Received on Tue Mar 26 2024 - 10:00:04 PDT
