Hi Kanin,

Yes. You can also find out what the charge is by running tleap once and
using the charge command, eg:
charge mol.4.O6
But checking the prep is fine too.


On Wed, Apr 25, 2018 at 1:23 PM, Kanin Wichapong <[log in to unmask]>

> Dear Rob and Oliver,
> Thank you so much for your helps and suggestions.
> Yes, I use the gag builder tool to build the heparin but first I have the
> problems about the naming and parameters of some residues (e.g. (UYS, QYS,
> and 6YS) that parameter of these residues cannot be found in
> GLYCAM_06j-1.prep and leaprc.GLYCAM_06j-1. Then, I use the updated glycam
> parameters (leaprc.GLYCAM_06k and GLYCAM_06k.prep) and parameters of these
> residues can be found in these new parameter files (leaprc.GLYCAM_06k and
> GLYCAM_06k.prep). However, I got another problems that the total charge is
> not 0. But I can solve the problems now.
> Just follow the tutorial as suggested by Oliver (
> derivatives-to-glycam-residues/). To summarize, I just have to change the
> charge of oxygen atom of the residue that is connected to the sulfate group
> by adding this value (+0.031) to the original value provided in the
> GLYCAM_06k.prep. Then, finally I have a heparin with the total charge is
> integer and equal to 0 after adding counter ions.
> Thank you very much,
> Kanin Wichapong