AMBER Archive (2005)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu May 19 2005 - 02:37:22 CDT

Hi Vijay,

You need to define the NEW parameters in a file (frcmod file) and load
that file into xleap with 'loadamberparams frcmod'. Check out the AMBER
parameter file to understand what I mean. And also read the following
webpage:

http://amber.scripps.edu/formats.html

Read the part which starts with "Force field parameter file
specification". It talks about how to create the frcmod file for your
system. For instance u have the following error message:

Could not find bond paramter for: CG - S

This means that the bond parameter (here its the average bond length) is
not defined for the atom type CG and S. (Check this out in the AMBER
parameter file u are loading in xleap, whether its there or not) The
same thing is also true for the other missing parameters, bond angle,
torsion, etc.

Hope this helps a little bit. I know its confusing, but try to understand
the frcmod file from the above link I gave to u. Also, read Ch.12 of the
AMBER 8 manual. It talks about how to define the new parameters, what they
mean, etc...

Good luck...

On Thu, 19 May 2005, Vijay Manickam Achari wrote:

> 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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