<p>I do command pdb2gmx but follow warning and error is came up:</p>
<p>WARNING: atom H is missing in residue GLY 1 in the pdb file<br> You might need to add atom H to the hydrogen database of residue GLY<br> in the file ff???.hdb (see the manual)</p>
<p>Fatal error:<br>There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing</p>
<p>my pdb file is:</p>
<p>HETATM 1 N GLY A 1 19.949 29.046 10.462<br>HETATM 2 CA GLY A 1 19.485 28.078 9.486<br>HETATM 3 C GLY A 1 20.152 28.247 8.136<br>HETATM 4 O GLY A 1 19.859 29.193 7.405<br>
HETATM 5 1H GLY A 1 20.545 29.773 10.181<br>HETATM 6 2HA GLY A 1 19.690 27.084 9.856<br>HETATM 7 2H GLY A 1 20.356 28.562 11.250<br>HETATM 8 3H GLY A 1 19.099 29.546 10.681<br>
HETATM 9 1HA GLY A 1 18.415 28.236 9.347</p>
<p>and my ffamber03.hdb of gly is</p>
<p>GLY 2<br>1 1 H N -C CA<br>2 6 HA CA N C</p>
<p>NGLY 2<br>3 4 H N CA C<br>2 6 HA CA N C</p>
<p>how I add H to hdb file?</p>