Leap Tutorial - Virus Dynamics

Amber 10 Tutorial
• 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.
On the next pages:
all commands will be underlined.
Units will be in bold.
filenames will be italisized
page references refer to Amber10Tools.pdf
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 >>source 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 >>bnr = loadpdb 1BNR1.jpdb
pg 46
– this loads the pdb 1BNR1.jpdb into the unit bnr
– units are what commands operate on in leap
• 3 >>addions 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 can’t be nuetralized with a positive ion.
Leap: add a protein and solvate
• 4 >>solvatebox 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 vanderwaal’s
radius between them and the solute by 25%. (allows the water to get a
bit closer to the solute.
• 5 >>savepdb bnr bnrwh2o.lpdb
pg 48
– bnrwh2o.lpdb is a pdb file generated by leap out of the unit bnr
• 6 >>saveamberparm bnr bnrwh2o.top bnrwh2o.crd
– saves the amber files for running sander.
– The order is always topology file then coordinate file.
pg 48
LEAP: Snapshot of bnrwh2o.lpdb
On saguaro@dnaseq in
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.
Other Leap Commands
• There are many other commands available in
– 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.