Sorry for the repeats. I do not see my posts being uploaded on the archive
and not sure if they are going through. Here are the two reply's I have
done since then:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Tried on Ubuntu and was much easier. One edit for this page:
http://ambermd.org/tutorials/basic/tutorial1/section2.htm on *"2.1.2)
Loading the structure into Leap*"
the command stated to put is "$AMBERHOME/exe/xleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB" but that is not a valid directory. I
did some searching around in the files and teh correct command is
"$AMBERHOME/AmberTools/src/leap/xleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB"
Thanks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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!
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Received on Sun Jan 27 2013 - 14:00:02 PST
