Hi all,<br>I'm trying to convert a .pdb file to a .gro file and the corresponding .top using pdb2gmx. The .pdb contains three subunits. The subunits are all the same protein, however each one is a different length (I'm assuming this is due to the experiment because that's how the file came from <a href="http://pdb.org">pdb.org</a>). Other than that, the subunits are identical (i.e. identical sequences). I start pdb2gmx with this command:<br>
<br>pdb2gmx -f tri_ABC.pdb -o tri_ABC -p tri_ABC -i tri_ABC -ignh -ff G53a6<br><br>I then get the following warnings:<br><br>WARNING: atom CG is missing in residue GLN 111 in the pdb file<br>WARNING: atom CD is missing in residue GLN 111 in the pdb file<br>
WARNING: atom OE1 is missing in residue GLN 111 in the pdb file<br>WARNING: atom NE2 is missing in residue GLN 111 in the pdb file<br>WARNING: atom HE21 is missing in residue GLN 111 in the pdb file<br> You might need to add atom HE21 to the hydrogen database of residue GLN<br>
in the file ff???.hdb (see the manual)<br>WARNING: atom HE22 is missing in residue GLN 111 in the pdb file<br> You might need to add atom HE22 to the hydrogen database of residue GLN<br> in the file ff???.hdb (see the manual)<br>
There were 6 missing atoms in molecule Protein_A<br><br>Now here's where it gets wierd. Residue 111 in all three subunits of my protein is SER, not GLN. I have no idea where the program is getting GLN, but it's only complaining about the 'extra' atoms that GLN has, but SER doesn't. <br>
<br>When I use the -missing option, I get a structure and a topology file that look ok. I do, however get similar warnings from the other two subunits. I end up with a total of 6 residues from the three subunits that pdb2gmx can't find atoms from because they are not the same residues as in my pdb. <br>
<br>Has anyone seen this before? Any ideas as to what could be causing this, or is it maybe a bug?<br><br>Thanks for your help<br>Gard Nelson<br>