On Sun, Jan 27, 2013, Jonathan Saboury wrote:
> So I am on XLEaP on Ubuntu now. Installed AmberTools12 correctly and all
> the tests seemed to have passed.
>
> I loaded this .pdb (http://pastebin.com/9ZMS3E6E) with "hexane1 = loadpdb
> "/home/jonathan/amber12/PDBs/hexane.pdb"
>
> and it outputs:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Loading PDB file: /home/jonathan/amber12/PDBs/hexane.pdb
> Unknown residue: PSD number: 0 type: Terminal/last
This is expected (on any OS). The xleap and tleap programs don't know
anything about chemistry, be it hexane or anything else. What these programs
basically do is bookkeeping: they compare atoms and residues in your PDB file
to atoms and residues in libraries that they have been told about, through
leaprc commands or through libraries users have loaded. If you don't load a
library and force field for hexane, LEaP can't do anything.
Standard amino acids and nucleic acids, and standard solvents like water, can
be loaded from pre-calculated libraries. See tutorial B4 for a discussion of
how to handle "general" organic molecules (like hexane, etc.)
....dac
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Received on Sun Jan 27 2013 - 15:00:03 PST
