Instructions to use Virtual Interaction Sites (VIS) for membrane and membrane-protein systems with the CHARMM force field. Note that for glycosylated proteins, additional parameter development is required. 


1) Build the system without VIS, for example using CHARMM-GUI, and run energy minimization without VIS.

2) If a protein is embedded in the membrane, separate the topology files and the structure files into two parts: one with only the membrane, and one with the protein.

3) Remove all water molecules from the structure files.

4) Make sure the structure files are in pdb format, and run them separately through pdb2gmx with the flag option -vsite hydrogens. This produces topology files and structure files for the system with VIS.
 
5) If you wish to use the modified topologies for VIS, with heavier hydrogen atoms for some acyl chain carbons, as described in the original paper, replace the topology files of the lipids generated by pdb2gmx with the modified topologies provided with this manual.

6) Recombine the topology files and the structure files (reassemble the system) and rehydrate.

7) Remember to use the charmm36-nov16.ff folder provided with this file set. It contains parameters for new types of VIS, and modifications of some existing VIS parameters.

Contact Himanshu KHandelia at hkhandel@sdu.dk if you have further questions.