[gmx-users] '+' and '-' sign in rtp file

[Justin A. Lemkul]

Chandan Choudhury wrote:
> I had a simple query regarding the rtp file . What does the '+' and '-' 
> sign indicates in the following dihedral inforamtion:
> 
>  [ dihedrals ]
>     CA     C    +N    +H    backbone_prop_1
>      O     C    +N    +H    backbone_prop_2
>     -C     N    CA    CB    backbone_prop_3
>     -C     N    CA     C    backbone_prop_4
>     CA     C    +N   +CA    backbone_prop_1
>      O     C    +N   +CA    backbone_prop_1

+ means next residue, - means previous.

> 
> Also, I cant understand the what is 'X' here in ffamberbon.itp:
> 
> X   C   C   X     3    30.33400     0.00000   -30.33400     0.00000     
> 0.00000     0.00000     ; new99
> X   C   O   X     3    23.43040     0.00000   -23.43040     0.00000     
> 0.00000     0.00000     ; new99
> X   C   OS  X     3    22.59360     0.00000   -22.59360     0.00000     
> 0.00000     0.00000     ; new99
> 

X means any atom type, if I recall.

-Justin

> 
> Chandan
> 
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> 

-- 
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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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