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galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry
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Topologies #11

Open simonbray opened 6 years ago

simonbray commented 6 years ago

Something we should add (maybe not urgently) is tools for producing topologies - Antechamber, PRODRG etc. Would be handy for simulating protein-ligand complexes for example.

simonbray commented 5 years ago

See also https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/24

chrisbarnettster commented 5 years ago

part way there with ambertools

  1. Choose any ligand (PDB or mol2)
  2. Run antechamber to parameterise and create mol2 format
  3. Run parmchk2 to check parms and create frcmod file (in txt)
  4. Build with tleap (not quite done but see https://www.cp2k.org/howto:biochem_qmmm . I have built with openmm (http://builder.openmm.org/) and will continue this.
  5. 💥 success
chrisbarnettster commented 5 years ago

progress made with galaxycomputationalchemistry/galaxy-tools-compchem#26 and galaxycomputationalchemistry/galaxy-tools-compchem#25