there are related questions.
the X is a wild card, and if there is no specific term that matches all 4
atom types, then the wild card matching the 2 middle atom types is used (in
the case you show, for the X-CT-CT-X dihedrals). it can be slightly more
complicated than that, but that should be a good start to help you
understand the files.
On Mon, Apr 13, 2015 at 9:20 AM, Jeffrey Teillet <jteillet.laas.fr> wrote:
> Hello,
>
> I'm a french student who's studying de parametrization of the
> ambertools14 software for the purpose of a work experience.
> I'm mailing you since you could help me understand some points.
>
>
>
> 1- " X -C -C -X 4 14.50 180.0 2. Junmei et al,
> 1999 "
>
> What does the X stand for in this sample of parm10.dat (dihedral angle)
> ? I've been searching but couldn't find any answers in the docs.
>
>
>
> 2- Still talking about dihedrals angles,
>
> RESI ARG
> " chi1 N CT CT CT "
> " chi3 CT CT CT N2 "
>
> I can't find some of the parameters in this parm10.dat file, like in
> this example (arginine residue). I don't know how those kind of dihedral
> angles are processed by AMBER since they just don't exist in the files
> or i can't find them.
>
>
> Thanks a lot for your upcoming answers (i hope), I can't wait for them,
> Best regards,
>
> J.Teillet
>
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>
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Received on Mon Apr 13 2015 - 07:00:04 PDT
