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.