[gmx-users] pdb2gmx bug?

[Gard Nelson]

Hi all,
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 pdb.org).  Other
than that, the subunits are identical (i.e. identical sequences).  I start
pdb2gmx with this command:

pdb2gmx -f tri_ABC.pdb -o tri_ABC -p tri_ABC -i tri_ABC -ignh -ff G53a6

I then get the following warnings:

WARNING: atom CG is missing in residue GLN 111 in the pdb file
WARNING: atom CD is missing in residue GLN 111 in the pdb file
WARNING: atom OE1 is missing in residue GLN 111 in the pdb file
WARNING: atom NE2 is missing in residue GLN 111 in the pdb file
WARNING: atom HE21 is missing in residue GLN 111 in the pdb file
         You might need to add atom HE21 to the hydrogen database of residue
GLN
         in the file ff???.hdb (see the manual)
WARNING: atom HE22 is missing in residue GLN 111 in the pdb file
         You might need to add atom HE22 to the hydrogen database of residue
GLN
         in the file ff???.hdb (see the manual)
There were 6 missing atoms in molecule Protein_A

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.

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.

Has anyone seen this before?  Any ideas as to what could be causing this, or
is it maybe a bug?

Thanks for your help
Gard Nelson
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