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Thank you Xiao and Lachele, I will refer this page.

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Naveen Kumar Vasudevan, Graduate student,
The Xi Research Lab,
Dept. of Chemical Engineering, McMaster University,
JHE- 296, 1280 Main St. W., Hamilton, ON L8S 4L7, Canada
Email: [log in to unmask] ; Tel: +1(647) 629-1562
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From: Lachele Foley
Sent: July 14, 2017 1:59 AM
To: [log in to unmask]
Subject: Re: SO3 group bond type for GLYCAM in LAMMPS - reg.

The page Xiao referenced is out of date (as it says at the top).

Use this one:  glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/


On Fri, Jul 14, 2017 at 1:22 AM, Xiaocong Wang <[log in to unmask]> wrote:
GLYCAM06 has bond types for both S and O2.  Bond length and angle parameters are also included in GLYCAM06.

Make sure you modify the atomic charges for the connecting oxygen atoms according to the following page:
http://glycam.org/docs/help/2014/04/04/sulfating-glycam-residues/
Sulfating GLYCAM Residues | Help for GLYCAM-Web
glycam.org
This information is out of date and retained here only for historical purposes. Use the information here at your own risk! These instructions apply to O-sulfation of ...



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 Naveen Kumar Vasudevan <[log in to unmask]>
Sent: Thursday, July 13, 2017 3:34:43 PM
To: [log in to unmask]
Subject: Re: SO3 group bond type for GLYCAM in LAMMPS - reg. 
 
No LAMMPS doesn't require specifications for bond order, just requires connectivity information, which I provide via a mol2 file ( it contains bond order). Yes, the partial charges are same it makes sense now, I just wanted to make sure whether the bond types were same or different as per GLYCAM.

Thank you for clarifying my doubt.




-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA