[gmx-users] gd_29 or gd_41 ?

2011-08-24 Thread Yun Shi 
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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Re: [gmx-users] gd_29 or gd_41 ?

2011-08-24 Thread Justin A. Lemkul 



Yun Shi 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
;



The comment here is incomplete.  See the 53a6 paper for a complete description.

-Justin


...

#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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