[HN Gopher] Leap - Chemistry Through a Computational Lens
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       Leap - Chemistry Through a Computational Lens
        
       Author : oumua_don17
       Score  : 47 points
       Date   : 2024-07-15 19:25 UTC (1 days ago)
        
 (HTM) web link (ambermd.org)
 (TXT) w3m dump (ambermd.org)
        
       | toddm wrote:
       | 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 wrote:
       | 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?
        
       | slashdave wrote:
       | Too bad that the PDB format is depreciated.
       | 
       | https://www.wwpdb.org/documentation/file-formats-and-the-pdb
        
         | toddm wrote:
         | 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."
        
           | slashdave wrote:
           | Come back when LEaP supports PDBX/mmcif.
        
       | flobosg wrote:
       | 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
        
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       (page generated 2024-07-16 23:01 UTC)