[gmx-users] pdb2gmx bug?

[Mark Abraham]

Gard Nelson wrote:
> 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 <http://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

No you're not "converting a .pdb to a .gro file" (which you don't ever 
need to do for normal usage), you are generating a molecular topology.

Also you should probably read the paper and/or comments associated with 
the .pdb file to understand the reason for the different lengths :-)

> 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. 

Where's the nearest GLN?

Mark

> 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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