1. Amber 10 Tutorial LEAP

2. 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. 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

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 >>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- 0pg 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.

5. Leap: add a protein and solvate 4 >>solvatebox bnr TIP3PBOX 12 0.75pg 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.lpdbpg 48 – bnrwh2o.lpdb is a pdb file generated by leap out of the unit bnr 6 >>saveamberparm bnr bnrwh2o.top bnrwh2o.crdpg 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@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.