[gmx-users] Re: gd_29 or gd_41 ?

[Yun Shi]

similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ?

#define gd_34     0.000       5.92          3
; -CHn,SI-CHn-    1.4
;
 ...

#define gd_40     0.000        1.0          6
; -CHn-C,NR(ring), CR1- 0.24
;
 ....

Something wrong with my interpretation of the comments after each
definition?

Thanks,

Yun Shi
On Wed, Aug 24, 2011 at 3:00 PM, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi,
>
> For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why
> would pdb2gmx automatically assign gd_29 ?
>
> In /gromos53a6.ff/ffbonded.itp, it appears:
>
> #define gd_29     0.000       3.77          3
> ; -C,CHn,SI-      0.9
> ;
>  ...
>
> #define gd_41     0.000       3.77          6
> ; -CHn-NT-  0.9
> ;
>  ...
>
> Thanks,
>
> Yun Shi
>
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