[gmx-users] cgnr in top file

[Justin A. Lemkul]

leila karami wrote:
> Dear Erik
>  
> thank for your answer.
>  
> my rtp file for amber 03 force field is as follow :
>  
> [ NGLY ]                            
>  [ atoms ]                          
>      N    amber99_39   0.29430     1
>     H1    amber99_17   0.16420     2
>     H2    amber99_17   0.16420     3
>     H3    amber99_17   0.16420     4
>     CA    amber99_11  -0.01000     5
>    HA1    amber99_28   0.08950     6
>    HA2    amber99_28   0.08950     7
>      C    amber99_2    0.61630     8
>      O    amber99_41  -0.57220     9
>  
> and my top file is as follow :
>  
> [ atoms 
> ]                                                                     
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
>      1 amber99_39      1   NGLY      N      1     0.2943      14.01  
>      2 amber99_17      1   NGLY     H1      2     0.1642      1.008  
>      3 amber99_17      1   NGLY     H2      2     0.1642      1.008  
>      4 amber99_17      1   NGLY     H3      2     0.1642      1.008   
>      5 amber99_11      1   NGLY     CA      3      -0.01      12.01   
>      6 amber99_28      1   NGLY    HA1      4     0.0895      1.008   
>      7 amber99_28      1   NGLY    HA2      5     0.0895      1.008   
>      8  amber99_2      1   NGLY      C        6     0.6163      12.01  
>      9 amber99_41      1   NGLY      O       7    -0.5722         16  
>  
> what relation is there between both of my rtp and top file in above ?
> 

When running pdb2gmx, the .rtp file is used to build the topology, assign 
charges and atom types, etc.  It looks like pdb2gmx is creating a single charge 
group for your N-terminal amine instead of placing each atom in individual 
charge groups.  The AMBER parameterization procedure did not use charge groups, 
so each atom is generally considered its own "group" for the purposes of running 
simulations in Gromacs.

-Justin

-- 
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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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