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Hi Tarsis,


I think you are right.  You need to alter the charge values after deleting HO4.  Please check the link in Oliver's response.  Make sure you check your structures with generated topology and coordinate files.


Best,


Xiao


Xiaocong Wang
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
E-mail: [log in to unmask]

From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Tarsis Gesteira <[log in to unmask]>
Sent: Sunday, December 10, 2017 10:23:42 AM
To: [log in to unmask]
Subject: how to generate paramaters for GlcNH3 oligodsaccharide
 
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