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
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
thank you
On Mon, Apr 7, 2014 at 3:12 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Apr 07, 2014, Lara rajam wrote:
>
> > I was able to proceed with all the commands, but the topology file is
> not
> > generated
> >
> > I have the following error
>
> ....your snippet didn't show any errors, just warnings. But there must
> have
> been errors, so look carefully in the leap.log file.
>
> >
> > O -SO 0.00 0.000 ATTN, need revision
> > SO-OS 0.00 0.000 ATTN, need revision
>
> This looks odd, since the atom types are in upper case, but gaff atom types
> are always lower case. There is almost certainly something wrong with the
> structure, or with the ways in which antechamber is identifying atoms
> types:
> did you ask for "-at amber"? (don't do that, unless you know your molecule
> has just the sorts of functional groups found in proteins or nucleic
> acids.)
>
> ...good luck...dac
>
>
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Received on Mon Apr 07 2014 - 13:30:05 PDT
