>Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>parameters. But for bon, you need to specify any bonded, angle, dihedral
>interaction that CB and CR61 have in your molecule.
The structure of these files is completely unclear to me. I also didn't find
any explanation of the
>Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>parameters. But for bon, you need to specify any bonded, angle, dihedral
>interaction that CB and CR61 have in your molecule.
The structure of these files is completely unclear to me. I also didn't find
any explanation of the
>Tom,
>
>Now before anything else..., do you need a CB to be defined? Doesn't
>one of the atom types present suffice? There's tyrosine in most force
>field already, you know, and these 'CB' atoms are merely part of the
>ring.
Indeed. If I just replace the CB and CR61 by C in the rtp file
and add
> Indeed. If I just replace the CB and CR61 by C in the rtp file
> and add the bondtypes using the G53a6bon.itp then PTR is defined as
> follows
Presumably you've checked some useful source that this carbon atom type is
reasonable to use for a tyrosine ring.
> WARNING 1 [file "sh2_pep.top", lin
4 matches
Mail list logo
