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
..relaxing end constraints to try for a dbase match
-no luck
Creating a new UNIT for residue: PSD sequence: 1
Created a new atom named: C01 within residue: .R<PSD 1>
...
Created a new atom named: H14 within residue: .R<PSD 1>
total atoms in file: 20
The file contained 20 atoms not in residue templates
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Then I type the command "saveamberparm hexane1 hexane.prmtop hexane.inpcrd"
and it outputs:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Checking Unit.
FATAL" Atom .R<PSD 1>.A<C01 1> does not have a type.
....
FATAL" Atom .R<PSD 1>.A<H14 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
How do I make it save the prmtop and inpcrd for this file? Thanks!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 27 2013 - 13:00:02 PST
