Thanks dor your reply.
I still want to use the ff03.r1 I was wondering which glycam version FF is
recommended for it?
And how to call/load it into tleap?
Thanks
On Fri, Mar 13, 2015 at 8:40 PM, Lachele Foley <lf.list.gmail.com> wrote:
> The 06j-1 files are tuned to work with ff12SB and later. You need to
> either use one of the other glycam leaprc varieties or use the other
> force field.
>
> This page has an explanation:
>
>
> http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/
>
> This page contains all the parameters:
>
> http://glycam.org/params
>
>
> On Fri, Mar 13, 2015 at 8:28 PM, Pedro Swagger
> <pedrito.swagger.gmail.com> wrote:
> > Hello everyone,
> >
> > I cannot load the modified residue for OLS (for O-linkages to SER), OLT
> > (for O-linkages to THR), and NLN (for N-linkages to ASN) into tleap
> > (AmberTools14). script below. When ever I try I get an error. Any other
> > residue is OK.
> >
> > Any idea what is wrong? Or I need to load something else.
> >
> > Thanks
> >
> > *************************************
> >
> > source leaprc.ff03.r1
> > source leaprc.GLYCAM_06j-1
> >
> > check OLT
> >
> >
> > Checking 'OLT'....
> > ERROR: The unperturbed charge of the unit: -0.194000 is not integral.
> > WARNING: The unperturbed charge of the unit: -0.194000 is not zero.
> > Checking parameters for unit 'OLT'.
> > Checking for bond parameters.
> > Could not find bond parameter for: N - CX
> > Could not find bond parameter for: CX - H1
> > Could not find bond parameter for: CX - 3C
> > Could not find bond parameter for: CX - C
> > Could not find bond parameter for: 3C - H1
> > Could not find bond parameter for: 3C - CT
> > Checking for angle parameters.
> > Could not find angle parameter: N - CX - H1
> > Could not find angle parameter: N - CX - 3C
> > Could not find angle parameter: N - CX - C
> > Could not find angle parameter: H - N - CX
> > Could not find angle parameter: CX - 3C - H1
> > Could not find angle parameter: CX - 3C - CT
> > Could not find angle parameter: CX - C - O
> > Could not find angle parameter: H1 - CX - 3C
> > Could not find angle parameter: H1 - CX - C
> > Could not find angle parameter: 3C - CX - C
> > Could not find angle parameter: 3C - CT - HC
> > Could not find angle parameter: 3C - CT - HC
> > Could not find angle parameter: 3C - CT - HC
> > Could not find angle parameter: H1 - 3C - CT
> > There are missing parameters.
> > check: Errors: 1 Warnings: 1
> >
> > --
> > Pedro
> >
> > Saludos
> >
> > Departamento de Física,
> > Facultad de Ciencias,
> >
> > Universidad de Chile
> > Las Palmeras 3425, Ñuñoa, Santiago, Chile
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pedro
Saludos
Departamento de Física,
Facultad de Ciencias,
Universidad de Chile
Las Palmeras 3425, Ñuñoa, Santiago, Chile
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Received on Sat Mar 14 2015 - 08:30:03 PDT
