Amber 10 Tutorial

1
Amber 10 Tutorial

• LEAP

2
LEAP

• You can open leap with two commands.
• xleap This opens a separate gui to run leap in.
• tleap This opens leap in the command prompt
• There is little difference between xleap and
  tleap as far as I can tell.

3
Leap

• On the next pages
• all commands will be underlined.
• Units will be in bold.
• filenames will be italisized
• page references refer to Amber10Tools.pdf

4
Leap add a protein and solvate

• Assume we have a pdb (1BNR1.jpdb) that we want
  to solvate add ions and water to, then get the
  amber coordinate and topology files from
• 1 gtgtsource leaprc.ff03 pg 52
• the default seems to be ff03. Other forcefields
  can be found on pg 14.
• You can source any file that has leap commands
  and leap will run those commands
• 2 gtgtbnr loadpdb 1BNR1.jpdb pg 46
• this loads the pdb 1BNR1.jpdb into the unit bnr
• units are what commands operate on in leap
• 3 gtgtaddions bnr Cl- 0 pg 38
• adds Cl- ions to the unit bnr in a random
  position within the vanderwaals distance away
  from the solute until the unit is nuetralized.
• If you put in Na into this particular system
  leap will not add ions and give a warning because
  bnr already positive and cant be nuetralized
  with a positive ion.

5
Leap add a protein and solvate

• 4 gtgtsolvatebox bnr TIP3PBOX 12 0.75 pg 50
• adds a solvent box of water around the unit bnr
  (remember bnr now has ions in it as well)
• The closest distance from the edge of the box to
  the solute in bnr will be 12 angstroms
• 0.75 means that the water molecules can go within
  the vanderwaals radius between them and the
  solute by 25. (allows the water to get a bit
  closer to the solute.
• 5 gtgtsavepdb bnr bnrwh2o.lpdb pg 48
• bnrwh2o.lpdb is a pdb file generated by leap out
  of the unit bnr
• 6 gtgtsaveamberparm bnr bnrwh2o.top bnrwh2o.crd pg
  48
• saves the amber files for running sander.
• The order is always topology file then coordinate
  file.

6
LEAP Snapshot of bnrwh2o.lpdb
On saguaro_at_dnaseq in /Quickgo/amber10tutorial/
bnrMD/ these files can be found. After
cleaning the directory by running delete.com try
the command tleap f bnr.leap This will run all
of these leap commands shown here immediately and
generate all of the needed files. a leap.log
file will also be generated detailing what leap
did.
7
Other Leap Commands

• There are many other commands available in leap.
• You can go to pg 3,4,5 in the Amber10Tools.pdf
  and see the commands listed and the page number
  at which you can find them in.