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:


Old, but maybe useful:


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

Best wishes,

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