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
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Received on Mon Apr 07 2014 - 15:30:08 PDT
