Dear Amber
Thank you , that tutorial is working good
I am able to generate the parameter files .
On Mon, Apr 7, 2014 at 6:00 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Apr 7, 2014 at 4:24 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > I can understand the gaff parameters are in lower case , thanks you for
> > your suggestion
> > but still i am not able to build the parameter it says the error as below
> >
>
> You didn't say what you actually did. Did you source leaprc.gaff? Did
> you run parmchk to generate an frcmod file from the mol2 in order to fill
> in missing parameters? Have you run this tutorial successfully:
> http://ambermd.org/tutorials/basic/tutorial4b/ ?
>
>
>
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Could not find angle parameter: s6 - os - ca
> > Could not find angle parameter: c - ca - os
> > Could not find angle parameter: c - ca - cc
> > Could not find angle parameter: ca - os - s6
> > Could not find angle parameter: ca - cc - ca
> > Could not find angle parameter: os - ca - cc
> > Could not find angle parameter: ca - os - s6
> > Could not find angle parameter: ca - os - s6
> > Building proper torsion parameters.
> > ** No torsion terms for ca-os-cc-ca
> > ** No torsion terms for ca-os-cc-ca
> > ** No torsion terms for os-cc-ca-c
> > ** No torsion terms for os-cc-ca-os
> > ** No torsion terms for os-cc-ca-ca
> > ** No torsion terms for os-cc-ca-ca
> > ** No torsion terms for c-ca-cc-ca
> > ** No torsion terms for ca-cc-ca-ca
> > ** No torsion terms for ca-cc-ca-ca
> > ** No torsion terms for os-ca-cc-ca
> > Building improper torsion parameters.
> > total 6 improper torsions applied
> >
> > How to fix these improper terms
> >
>
> These are missing angles and dihedrals, NOT missing improper torsions.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 08 2014 - 08:00:05 PDT
