AMBER Archive (2005)

Subject: AMBER: parameter for sulfur in thio-glucoside residue

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Wed May 18 2005 - 20:58:57 CDT

Hi to all amber users,
I am attempting to model micelle sturcture with using
thio-beta-octyl-D-glucopyranoside residue.
For that I tried to model a single residue of
thio-beta-octyl-glucopyranoside using xleap editor.
I have also changed to atom type for sulfur S.

After model I tried to save the single residue using
SAVEAMBERPARM command.
But it failed to save.
It says improper torsion angles.....
S-CT-...
CT-S....
  
How I should solve this problem?
Where do I can get the parameter for sulfur and
glucopyranoside head of sugar? (because the sulfur
atom is linking atom between head and tail of the
atom)
 
What should I do to overcome this error?
  
Can any one there help me?
Thank you very much
With high hope.
Vijay Manickam Achari

        
        
                
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