Dear GLYCAM ,

I built a glycoprotein in www.glycam.org, the following is the sequence of glycan, this glycan will be loaded on an N-link site.

DNeup5Acb2-6DGlcpNAcb1-2DManpa1-3[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-OH

I'm having two problems right now：

1. After I built the glycoprotein, I read it using amber-tleap, and its charge was not an integer after loading the force field, which made the tleap report a warning. Here's the force field I use：
source leaprc.GLYCAM_06j-1
source leaprc.protein.ff19SB
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
 
Then there's the tleap warning message：
saveamberparm RBD RBD.prmtop RBD.inpcrd
Checking Unit.

Warning: The unperturbed charge of the unit (1.194000) is not integral.

Warning: The unperturbed charge of the unit (1.194000) is not zero.

Note: Ignoring the error and warning from Unit Checking.

I'm pretty sure this is the problem with glycans because the charge of the protein is 2

2. After tleap reads the glycoprotein, tleap automatically adds hydrogen atoms, resulting in extra hydrogen on the nitrogen atoms of the glycan and asparagine-amide groups， but PDB files with hydrogen atoms output on www.glycam.org do not have this problem, I wonder if this will have any adverse effect on the results.

Kind regards,
Lan Wei