Setting Up Membrane Protein Simulations

The Tutorial for this Workshop can be found here

MemProtMD Package

For ease unpack in your home directory.

tar xvf MemProtMD.tar.gz
cd MemProtMD/AT2CG/

Both Memembed and DSSP (included in the archive) require Boost. You should also be able to install DSSP via apt-get on Linux (eg Ubuntu):

tar xvf dssp-2.2.1.tar
tar xvf memembed.tar
sudo apt-get install libboost-all-dev libbz2-dev dssp

Mac

tar xvf dssp-2.2.1-mac.tar
tar xvf memembed-mac.tar
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install boost

Then compile Memembed and DSSP:

cd dssp-2.2.1
make

cd ../memembed
make

Software Requirements

Gromacs (5.0 +)

Quick and dirty installation should work:

tar xfz gromacs-5.0.6.tar.gz
cd gromacs-5.0.6
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

MDAnalysis

sudo easy_install -U setuptools
sudo easy_install pip
pip install MDAnalysis

Pymol

In Ubuntu:

sudo apt-get install pymol

Additional Packages:

VMD is also useful.
As is PDB2PQR:

Ubuntu:

sudo apt-get install pdb2pqr

* Pulchra allows full conversion.

Package Details:

MemProtMD (AT2CG)

To convert to Martini CG (http://cgmartini.nl/) and set-up a random box of lipids.

perl at2cg.pl protein.pdb 1 popc

or eg:

perl at2cg.pl protein.pdb 2 popc 25 pope 75

The following variables need to be set for at2cg to work:

The directory containing the atomistic fragments and tip files:
```
$shared = "~/MemProtMD/AT2CG";
```
Location for Gromacs:
```
$gromacs = "/usr/local/gromacs/bin";
```

You can also break this down into:

python ~/MemProtMD/AT2CG/martinize.py -f protein.pdb  -merge all -dssp ~/MemProtMD/AT2CG/dssp-2.2.1/mkdssp -ff martini22 -v -x protein-cg.pdb -o protein-cg.top -elastic -ef 1000 -el 0.5 -eu 0.9 -ea 0 -ep 0
perl ~/MemProtMD/AT2CG/add-lipids.pl 1 popc

Again for add-lipids.pl you need to specify:

The directory containing the atomistic fragments and tip files:
```
$shared = "~/MemProtMD/AT2CG";
```
Location for Gromacs:
```
$gromacs = "/usr/local/gromacs/bin";
```

CG2AT

To convert the system back to atomistic use the cg2at.pl script:

perl cg2at.pl cg.pdb GPCR.pdb

The following variables need to be set for cg2at to work:

The directory containing the atomistic fragments and itp files
```
$cg2atdir = "~/MemProtMD/CG2AT";
```
Location for Gromacs
```
$gromacs = "/usr/local/gromacs/bin";
```
Location for Pymol (including executable)
```
$pymol = "/usr/local/bin/pymol";
```
Ideally also provide the protein-cg.itp file that details the CG protein parameters, the name of this file can be modified within the script itself.

Options (You don't need to change):

CG Protein itp file
```
$itp = "protein-cg.itp";
```
Number of individual proteins (multiples of protein-cg.itp) - Do not change unless your system includes>=2 proteins and you wish to use the alignment mode. Alignment mode doesn't work for heteromers in separate itp files.
```
$protnum = 0;
```
Lipid deletion method - alchembed, pymol, genbox, g_membed or none - (required for "align" method). You can often get away with "none" but otherwise its alchembed < pymol< g_membed< genbox in terms of increasing numbers of lipids deleted.
```
$deletion = "alchembed";
```
Delete Waters? - gmxsolvate, pymol, waterkiller or none. Pymol/gmxsolvate work best.
```
$delete_waters = "gmxsolvate";
```
Optimise Box? Only works if Bilayer has formed along xy plane. Reduces the size of enormous systems.
```
$optimise = "yes";
```
Align the original protein with just the TM domains or all residues (tm/all)
```
my $align = "tm";
```
Merge Chains? - useful if inter-subunit disulphide is required (yes/no).
```
my $merge = "no";
```

Wiki

CECAM-Setup / MemProtMD Pipeline