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Hi Kanin,

If you are doing this through tleap, you must adjust the charge on the atom
you connect the sulfate to. See here for details:

http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/

Old, but maybe useful:
http://glycam.org/old/pages/sulfation.html

Oliver

On Tue, Apr 24, 2018 at 7:58 PM, Rob Woods <[log in to unmask]> wrote:

> Hi Kanin,
> Try using the gag builder tool: http://glycam.org/tools/
> molecular-dynamics/oligosaccharide-builder/build-glycan?id=8
>
> Best wishes,
> Rob
>
> Excuse the brevity, sent from iPhone
>
> On Apr 24, 2018, at 1:17 PM, Kanin Wichapong <[log in to unmask]>
> wrote:
>
> Dear Sir,
>
> I tried to generate the parameters for Fondaparinux (Arixtra), in which
> the sequence is D-GlcNS6S-α-(1,4)-D-GlcA-β-(1,4)-D-GlcNS3,6S-α-(1,4)-L-IdoA2S-α-(1,4)-D-GlcNS6S-OMe,
> by using GLYCAM web server.  First, I had the problems that residue UYS,
> QYS, and 6YS don't have parameters in the GLYCAM_06j-1.prep  file.
> However, I found updated parameters for GLYCAM  (GLYCAM_06k.prep) and all
> parameters for these residues can be found in leaprc.GLYCAM_06k.  But then
> I have another problems during tleap (in AMBER), I got this warning about
> charges
>
> ERROR: The unperturbed charge of the unit: -0.155000 is not integral
> WARNING: The unperturbed charge of the unit: -0.155000 is not zero.
>
>
> So, how to fix this problem or the parameters of Fondaparinux for running
> MD simulations in AMBER are available somewhere? I tried to find available
> parameters for this heparin but I couldn't find it.
>
> Any helps or suggestions will be very appreciated.
>
> Thank you so much in advance.
>
> Best Regards,
> Kanin Wichapong
>
>