Hi Tarsis,

After you removed H4O, O4 would be "Oh" atom type.  It will be "Os" atom type to be able to connect to another sugar.

Use the following command after "remove" command:

set m.3.O4 type Os



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: Tuesday, December 12, 2017 12:43:46 AM
To: [log in to unmask]
Subject: Re: how to generate paramaters for GlcNH3 oligodsaccharide

Thanks a lot!

I think I'm getting closer - this is the input

 source leaprc.GLYCAM_06j-1
 loadamberprep GlcNH2_and_GlcNH3.prep
 loadamberparams glcnh3.frcmod
 m = sequence { ROH 4ZB 0YNP }
 remove m m.3.H4O
 set m tail m.3.O4
 set m.3.O4 charge -0.433
 m = sequence { m 4ZB 0YNP }
 saveAmberParm m 1.prmtop 1.crd
 savepdb m 1.pdb

and the output:

Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: Cg - Oh - Cg
Building proper torsion parameters.
 ** No torsion terms for  Cg-Cg-Oh-Cg
 ** No torsion terms for  Cg-Oh-Cg-H2
 ** No torsion terms for  Cg-Oh-Cg-Os
 ** No torsion terms for  Cg-Oh-Cg-Cg
 ** No torsion terms for  H1-Cg-Oh-Cg
 ** No torsion terms for  Cg-Cg-Oh-Cg
Building improper torsion parameters.
old PREP-specified impropers:
 total 2 improper torsions applied
 0 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.

for some reason, the parameters are not there.

Would anyone know where could I find those?

Thanks in advance,