Hi,
I am new to AMBER
The default message on xleap window goes like this..
Welcome to LEaP!
Sourcing leaprc: /usr/local/amber6/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /usr/local/amber6/dat/parm94.dat
Loading library: /usr/local/amber6/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber6/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber6/dat/leap/lib/water.lib
>
At the prompt, I typed "edit methane" then new window pops up for drawing.
I created a molecule (methane) on it and finished the drawing
by choosing "Add H & Build". Then I checked the unit with "Chek unit".
The message says that
Unit Editor: Added missing heavy atom: .R<methan 1>.A<C1 1>
Unit Editor: Added missing heavy atom: .R<methan 1>.A<C2 2>
Unit Editor: (used 7 default bond params)
Unit Editor: (used 12 default angle params)
Unit Editor: (used 9 default torsion params)
Unit Editor: > check methan
Unit Editor: Checking 'methan'....
Unit Editor: FATAL: Atom .R<methan 1>.A<C1 1> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<C2 2> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H3 3> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H4 4> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H5 5> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H6 6> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H7 7> does not have a type.
Unit Editor: FATAL: Atom .R<methan 1>.A<H8 8> does not have a type.
Unit Editor: Checking parameters for unit 'methan'.
Unit Editor: Checking for bond parameters.
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Could not find bond parameter for: -
Unit Editor: Checking for angle parameters.
Unit Editor: Could not find angle parameter: - -
Unit Editor: Could not find angle parameter: - -
Unit Editor: There are missing parameters.
Unit Editor: check: Errors: 8 Unit Editor: No atoms selected
What is wrong here ?
It looks to me that the atom type could not defined automaticaly.
I choosed "edit selected atoms" and the table has "type" column and the
column is missing. Do I have to defined evey atom type MANUALLY ?
Or is there any method that this could be done automatically ?
Thank you.
Soonmin
PS. One more question. Can I magnify the drawings on xleap ?
Received on Sun Oct 21 2001 - 16:55:17 PDT
