[gmx-users] amber force field in gromacs

[Mark Abraham]

leila karami wrote:
> dear Mark
>  
> my command is: pdb2gmx -f c.pdb -p c.top -o c.gro .
>  
> I think what I'm doing is clear. also there is GLY 1 :
>  
> pdb file of GLY 1                     
>                                      
> 1  N  NGLY  1                        
> 2  CA NGLY  1                        
> 3  C  NGLY  1                        
> 4  O  NGLY  1                        
> 5 1H  NGLY  1                        
> 6 2HA NGLY  1                        
> 7 2H  NGLY  1                        
> 8 3H  NGLY  1                        
> 9 1HA NGLY  1                        

Residue 1 named NGLY is not the same thing as residue 1 named GLY. I 
can't reconcile pdb2gmx complaining about residue 1 named GLY if c.pdb 
file names residue 1 as NGLY.

Mark

> rtp file of GLY 1                     
>                                      
> [ 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 
>