AMBER Archive (2005)

Subject: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu May 19 2005 - 01:55:21 CDT

Dear amber users, when I tried to use saveamberparms,
I get the output as below.

> saveamberparm thio thio.top thio.crd
Checking Unit
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond paramter for: CG - S
Building angle parameters.
Could not find angle parameter: H2 - CG - S
Could not find angle parameter: CG - S - CT
Could not find angle parameter: OS - CG - S
Could not find angle parameter: CG - CG - S
Building proper torsion parameters.
* * No torsion terms for H2-CG-S-CT
* * No torsion terms for OS-CG-S-CT
* * No torsion terms for CG-OS-CG-S
* * No torsion terms for H1-CG-CG-S
* * No torsion terms for CG-CG-S-CT
* * No torsion terms for OH-CG-CG-S
Building improper torsion parameter.
old PREP-specified impropers:
 total 0 improper torsions applied
 0 improper torsions in old prep form
Building H-Bond paramters
Parameter file was not saved.

--- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> Hi Vijay,
>
> Can u copy/paste the error message u are getting?
> And also the residue
> that u have created in xleap. I would guess that you
> need to define
> the improper torsion angles in your modified frcmod
> file in order xleap
> to understand the new structure.
>
> On Thu, 19 May 2005, Vijay Manickam Achari wrote:
>
> > 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
> >
> >
> >
> >
> >
> >
>
___________________________________________________________
> Ilyas Yildirim
http://www.pas.rochester.edu/~yildirim/

        
        
                
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