<div>dear Mark</div>
<div> </div>
<div>my command is: pdb2gmx -f c.pdb -p c.top -o c.gro .</div>
<div> </div>
<div>I think what I'm doing is clear. also there is GLY 1 :</div>
<div> </div>
<div>pdb file of GLY 1 <br> <br>1 N NGLY 1 <br>2 CA NGLY 1 <br>3 C NGLY 1 <br>4 O NGLY 1 <br>
5 1H NGLY 1 <br>6 2HA NGLY 1 <br>7 2H NGLY 1 <br>8 3H NGLY 1 <br>9 1HA NGLY 1 <br> <br>
rtp file of GLY 1 <br> <br>[ NGLY ] <br> [ atoms ] <br> N amber99_39 0.29430 1 <br> H1 amber99_17 0.16420 2 <br>
H2 amber99_17 0.16420 3 <br> H3 amber99_17 0.16420 4 <br> CA amber99_11 -0.01000 5 <br> HA1 amber99_28 0.08950 6 <br> HA2 amber99_28 0.08950 7 <br> C amber99_2 0.61630 8 <br>
O amber99_41 -0.57220 9 </div>