Hi Tarsis,

This will help with setting charges:
http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/

I've never used the GlcNH2_and_GlcNH3.prep files and don't know where you got them, so can't check. This part looks wrong:
 glycan = sequence { ROH 4ZB 0YNP }
 set glycan tail glycan.3.O4

Do you not have a 4YNP available? The 0.194 charge is due to attaching to the 0YNP. Perhaps the suggestion is to adjust the charge on the O4 by 0.194. See the link for how to do that.



Oliver

On Sun, Dec 10, 2017 at 4:23 PM, Tarsis Gesteira <[log in to unmask]> wrote:
Hi all,

While trying to build a hexasaccharide using leap and GlcNH2_and_GlcNH3.prep.

 source leaprc.GLYCAM_06j-1
 loadamberprep GlcNH2_and_GlcNH3.prep
 loadamberparams glcnh3.frcmod
 glycan = sequence { ROH 4ZB 0YNP }
 set glycan tail glycan.3.O4
 glycan = sequence {glycan 4ZB 0YNP }
 saveAmberParm glycan glycam.prmtop glycam.crd
 savepdb glycan glycam.pdb

 I was told that I need to delete the HO4 and alter the charge, as I was getting this error:

> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.194000 is not integral.
> WARNING: The unperturbed charge of the unit: 0.194000 is not zero.

May I get some help on how to properly do this?

Thanks in advance,

Tarsis