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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