[gmx-users] [Fwd: pdb UNK residue]
Mark.Abraham at anu.edu.au
Thu Aug 23 05:32:23 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.
It's a residue topology database. From the foregoing, I don't think
you've read chapter 5 of the manual, like I suggested last time. In
particular, section 5.5.1 explains the use and abuse of the .rtp files,
and there's more you need to have read before you can ask sensible
questions about what to do here.
There are no standards for residue and/or molecule abbreviated names,
because there are many more molecules than possible names. If you want
to use automated topology builders like pdb2gmx, then you need to have
your input structure names conform to the .rtp for the force field
you're using - that's all.
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