[gmx-users] amber force field in gromacs

[leila karami]

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

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
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