[gmx-users] Re: gd_29 or gd_41 ?

[Justin A. Lemkul]

Yun Shi wrote:
> 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?

No, but the comments are somewhat shorthand.  There's nothing wrong here, 
either.  CG is a planar carbon.  CHn is a tetrahedral center.  So even though CG 
is not of type CR1, the dihedral is still correct, geometrically speaking.

-Justin

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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