Dear all,<br><br>I am trying to use amber03 force field. I corrected the amino acid names as described on <a href="http://chemistry.csulb.edu/ffamber/">http://chemistry.csulb.edu/ffamber/</a>. <br><br>However, when I ran pdb2gmx on a PDB file without H-atoms, I got the following error:<br>
<br>pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb<br><br>...<br>WARNING: atom H is missing in residue THR 1 in the pdb file<br> You might need to add atom H to the hydrogen database of residue THR<br>
in the file ff???.hdb (see the manual)<br><br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.2<br>Source code file: pdb2top.c, line: 701<br><br>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<br>
-------------------------------------------------------<br><br>I checked the ffamber03.hdb. It is in the correct directory as other *.hdb files. It also contains the entry for H-atom in THR:<br><br>THR 5<br>1 1 H N -C CA<br>
1 5 HA CA N CB C<br>1 5 HB CB CA CG2 OG1<br>3 4 HG2 CG2 CB CA<br>1 2 HG1 OG1 CB CA<br><br>Can anyone tell me what might be the problem? I should be able to use pdb2gmx and amber03 to add all H-atoms, right?<br>
<br>Thanks!<br><br>Peggy<br>