After having all the files needed for the protein, we are left with preparing the required files for our membrane system.

For this tutorial, we obtained our membrane through CAHRMM-GUI, making a POPC/POPG membrane with 80:20 lipids respectively and having a 15 angstrom water layer. In CHARMM-GUI we have asked for the program to write all files needed for a GROMACS setup and we have extracted the pdb for the final assembly of the protein, the .itp files for each lipid, and the topology of the membrane system. These are the required files for the implementation of our membrane system in our CpHMD simulation.

This process has a couple of tricks to make it work on our CpHMD construction, which will be discussed below:

1. Changing the lipid and water residue name.

[!caution] CpHMD has a limit of 3 characters in the residue name. Unfortunately, this limitation clashes with the lipid naming which usually resorts to 4 letters.

As of now, the CpHMD PB/MC calculation requires all the solute names to be at most 3 characters long.

quick steps

1. get .itp files from CHARMM-GUI folder

2. get membrane pdb from charmm-folder

3. get membrane top from charmm-gui folder

4. Add the lipid number, waters and ions to the topology

5. change lipid names to have 3 letters only in the itp pdb and top files.

6. add-mol-db app run to get the database parameters.

7. add the new parameters to the delphi databases extracted.

System Preparation Steps

1. Open both protein and membrane pdb structures and put the peptide inside the system box. (saving the file must not reorder the atom names! or it will crash)
2. index building
3. minimization
4. initialization

TO edit still

  Membrane Preparation

For the membrane preparation you will need to have:

• pdb/gro file with hydrated membrane
• topology of that membrane
• itp files with the parameters for the lipids.

  I. Adding the peptide structure to the membrane system

This step consists on adding the peptide obtained in the Peptide Preparation step into the hydrated membrane system. To do so you need to open both the peptide gro file from the pdb2gmx and the membrane system in your preferred molecular viewing software (pymol, VMD, etc).

After dragging the peptide into the membrane system box, in the water phase, you should save the complete structure as a new file and then reconvert it back into gro. This will be the gro to be used for the minimization and initialization of the system.

[!Note] If you don't have a GROMACS compilation in your system, you can convert the pdb to gro with the container with: singularity run --bind <current directory> CpHMD.sif gmx editconf -f <pdb complete file>.pdb -o <output complete gro>.gro -resnr 1

  II. Completing the peptide topology with membrane information

[!warning] Currently CpHMD only supports 3 letter code residues. Hence, lipids who typically have 4 letter codes need to have their residue name changed on the .itp file to comply with the 3 letter code

This also needs to be changed on the structure file obtained in the previous step, editing the 4 letter lipid name to the chosen 3 letter name

To complete the topology of the peptide obtained in the Peptide Preparation, we will need to add the information of the membrane.

First, the lipid itps should be included in the topology:

#include "./CHARMM36pH.ff/.itp"  

Secondly, the correct number of molecules of each type in your structure file needs to be corrected in the [ molecules ] section at the end of the topology.

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