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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