Leap – Chemistry Through a Computational Lens

https://ambermd.org/tutorials/pengfei/index.php

by oumua_don17 • 2 years ago

56 6 2 years ago

toddm2• 2 years ago

Great to see LEaP (and AMBER) on the front page of HN!

Note that LEaP is one part of the AmberTools suite of programs and is used to prepare systems for subsequent molecular dynamics simulations.

- Long-time AMBER disciple/user

vapemaster• 2 years ago

not hating on the great amber - but why LEaP on the front page of HN with no context...?

happy to see some light shown on the grim state of comp chem file formats and their shockingly lossy interconversion but I'm not sure that was the OP's intent?

slashdave2• 2 years ago

Too bad that the PDB format is depreciated.

https://www.wwpdb.org/documentation/file-formats-and-the-pdb

toddm2• 2 years ago

What does deprecation of an upstream file format - still the most widely-used one, by the way - have to do with support of said format by someone else's software? If anything, it illustrates backward compatibility. And it has nothing to do with a web page describing the use of LEaP. Your comment is simply not germane.

LEaP supports the mol2 format as illustrated in the OP's link, which is substantially better than the PDB format; but again, this thread has nothing to do with file formats and everything to do with the functionality of LEaP.

Finally, it's "deprecated," not "depreciated."

slashdave2• 2 years ago

Come back when LEaP supports PDBX/mmcif.

flobosg• 2 years ago

Fun fact: LEaP’s original author, Christian Schafmeister, went on to create a Common Lisp implementation that uses C++ and LLVM for applications in molecular nanotechnology: https://www.youtube.com/watch?v=8X69_42Mj-g

Leap – Chemistry Through a Computational Lens

Related Stories