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Amber 10 Tutorial

Amber 10 Tutorial. LEAP. 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. . Leap. On the next pages:

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Amber 10 Tutorial

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  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 >>sourceleaprc.ff03pg 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 = loadpdb1BNR1.jpdb pg 46 • this loads the pdb 1BNR1.jpdb into the unit bnr • units are what commands operate on in leap • 3 >>addionsbnrCl- 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.

  5. Leap: add a protein and solvate • 4 >>solvateboxbnr 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 >>savepdbbnrbnrwh2o.lpdb pg 48 • bnrwh2o.lpdb is a pdb file generated by leap out of the unit bnr • 6 >>saveamberparmbnrbnrwh2o.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@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.

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