[gmx-users] [Fwd: pdb UNK residue]
Dallas B. Warren
Dallas.Warren at vcp.monash.edu.au
Thu Aug 23 05:29:01 CEST 2007
> Thank you for your answer.
> But I still need to make something clear.
> If I understand it right, UNK is unknown.
> It means parts of molecules are not defined, possibly, atoms.
> HETATM 1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0
> HETATM 2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0
> HETATM 3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0
> HETATM 4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0
> Names of these parts should be in rtp file (without
> explanations). These parts should be defined like variables
> in programming. It means I need to know names of such parts.
> To know it, I need a list of names of all parts with their
> explanations. This is what I want to find. It would be good
> if you confirm that I am right or not. And if I am right,
> could you please, inform me where to take the list of names
> of the parts with their explanations. Thank you in advance.
Forth column in PDB format refers to the residue name. As already
indicated, it doesn't matter what you call it, you can call it XXX if
you like or even ABC, it simple doesn't matter in YOUR case (which is
for a small molecule). It is just a label, which will not be used in
any real meaningful way, other than a label for that residue.
If you were dealing with a residue within a protein or some other larger
molecule, which you are not, then it would matter when you are building
the topology file using pdb2gmx, as that is used by the script to assist
in constructing it.
But for you, since it is a small molecule, it does not matter. You do
not have to use pdb2gmx on a small molecule. pdb2gmx uses the .rtp
file, but since you don't need to use pdb2gmx, then doesn't matter that
the residue is not within the .rtp file. The URLs you were directed to
indicate this, as does the GROMACS manual. I would suggest that you
read through the links you have been previously supplied with again
carefully, and the GROMACS manual, particularly Chapter 5.
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