You need to create a parameter file with these parameters. You will need to
either obtain these parameters from published work, fit them yourself or
make a reasonable guess.
See
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
for a tutorial on how to create an frcmod file containing missing
parameters.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Vijay Manickam Achari
> Sent: 18 May 2005 23:55
> To: amber.scripps.edu
> Subject: AMBER: the out put I get... parameter for sulfur in
> thio-glucoside residue
>
> 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.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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Received on Thu May 19 2005 - 08:53:00 PDT
