Explicit membrane

HADDOCK
4

The resnames that are in the library are the ones that HADDOCK can natively support without third-party applications. Meaning they should work out-of-the box in your local installation.

Via the web interface, topologies and parameters are automatically generated using PRODRG for residues that are not part of the library. This is unfortunately is a server-side only feature and you must go via the web interface to use it.

If you’d like to use the PRODRG generated parameters in a local run, that would be possible with some tweaking - check out this post here. You could do something similar for HADDOCK2.4;

  1. setup a refinement run with your membrane complex
  2. download the input files and copy the ligand.top/ligand.par/ligand.pep somewhere
  3. setup a local run
  4. copy the server generated top/par to the cloned topology run directory (usually run1),
$ cat ligand.top >> run1/toppar/ligand.top
$ cat ligand.par >> run1/toppar/ligand.param
$ cat ligand.pep >> run1/toppar/ligand.pep

That should do the trick, good luck! (: