[gmx-users] cgnr in top file

[Erik Marklund]

The last column in your rtp entry holds the chargegroup numbers. The 
cgnr column in your top file looks just like it. Amber03 was not 
parameterized with charge groups, so the atoms are not groupt together 
as you can see.

Erik

leila karami skrev:
> 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 ?


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/