Your molecule does not seem as complex.
All bond, angle, torsion and improper torsion
parameters are available in the GAFF library at
$AMBERHOME/amber8/dat/leap/parm/gaff.dat
Construct and pre-minimize your molecule in leap.
save the molecule in pdb format in leap as mol.pdb.
(i.e.; savepdb mol mol.pdb)
Exit leap.
Now, you need to convert your pdb file to a mol2 file
by antechamber.
Assuming that your molecule has zero net charge,
run antechamber as
$AMBERHOME/exe/antechamber -i mol.pdb -fi pdb -o
mol.mol2 -fo mol2 -at gaff -c bcc -nc 0 -rn MOL -j 5
...takes about a couple of minutes.
After the antechamber job is done, take a close look
at the mol.mol2 file in the current directory. Note
that atom types are recorded in lowercase, and also
you should have AM1-BCC partial atomic charges in the
mol2 file ready for energy computations.
Re-execute leap
load in the GAFF library as
source leaprc.gaff
load in your mol2 molecule in leap as
mol=loadmol2 mol.mol2
create prmtop and x files as
saveamberparm mol mol.prmtop mol.x
quit
hope this works for you..
jenk..
--- Vijay Manickam Achari <vjrajamany.yahoo.com>
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.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 - 18:53:01 PDT
