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
Received on Fri Mar 13 2015 - 18:00:02 PDT
