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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