[gmx-users] amber force field in gromacs

[leila karami]

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:
*
*
NGLY 2
3   4 H    N     CA   C
2   6 HA  CA   N     C

I didn't use -missing option.

please guide me.
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