is there any chance to use HADDOCK with explicit membrane (i.e. Phosphatidylcholine DDPC) and not just the coarse representation as shown in the tutorial? I mean, the full lipid chain. I could not find the resname in the library name. Or just set it as HETATM?
The server can indeed handle explicit lipids defined as HETATM.
I have seen e.g. nanodisks submitted to the server and running fine.
Local installation? I am trying it anyway … just out of curiosity. I have a DDPC membrane from CHARMM-GUI.
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;
- setup a refinement run with your membrane complex
- download the input files and copy the
- setup a local run
- copy the server generated top/par to the cloned topology run directory (usually
$ 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! (: