[gmx-users] amber force field in gromacs

[Mark Abraham]

leila karami wrote:
> Hi
> 
> I used amber03 force field in gromacs to study pr-dna interaction.
> I compare my pdb file and ffamber03.rtp file.
> I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 
> 1) and C-terminal (NUMBER 70) of my protein is GLY.
> pdb file and rtp file relating to gly1 and gly70 are placed in follow.
> 
> pdb file of gly1:
> 
> 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
> 
> rtp file of gly1:
> 
> [ 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
> 
> pdb file of gly70:
> 
> 1  N   CGLY A  70
> 2  CA  CGLY A  70
> 3  C   CGLY A  70
> 4  O   CGLY A  70
> 5  H   CGLY A  70
> 6 2HA  CGLY A  70
> 7 1HA  CGLY A  70
> 8  OXT CGLY A  70
> 9      CGLY A  70
> 
> rtp file of gly70:
> 
> [ CGLY ]
>  [ atoms ]
>      N    amber99_34  -0.38210     1
>      H    amber99_17   0.26810     2
>     CA    amber99_11  -0.24930     3
>    HA1    amber99_19   0.10560     4
>    HA2    amber99_19   0.10560     5
>      C    amber99_2    0.72310     6
>    OC1    amber99_45  -0.78550     7
>    OC2    amber99_45  -0.78550     8
> 
> before correction of pdb file, following warning and error was came up:
>  
> *WARNING: atom H is missing in residue GLY 1 in the pdb file
>          You might need to add atom H to the hydrogen database of 
> residue GLY
>          in the file ff???.hdb (see the manual)
> *
> *Fatal error:
> There were 1 missing atoms in molecule Protein_A, if you want to use 
> this incomplete topology anyhow, use the option -missing
> *
> ffamber03.hdb:
> * *

I don't understand what you're doing. There is no GLY 1 in the above.

Please describe the contents of your .pdb file and give your pdb2gmx 
command line.

Mark

> NGLY 2            
> 3   4 H    N     CA   C
> 2   6 HA  CA   N     C
> 
> I didn't use -missing option.
> 
> please guide me.
>