MemGen creates multi-component lipid bilayer membranes for molecular dynamics simulations.

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Help

Some basic tips are listed below. If you need additional help or if something is unclear, please contact us.

Running an Example Job

If you are using MemGen for the first time, try running through this example to get acquainted with the system:

  • Download one or more of the following lipid files: Charmm POPS, Amber DOPC, Berger POPE, Berger POPC, Gromos-CKP Lipid-A.
  • Upload your chosen files to MemGen, clicking Add Lipid as necessary.
  • Choose your desired molar fractions, salt NaCl concentration, and lipids per monolayer. Leave the area per lipid value as default.
  • Hit Submit. The system will process the job and present a preview render with a link for downloading the results.

Received and error?

The most common error you may encounter is a message such as acpype ended with non-zero exit code or Antechamber ended in error. This means that MemGen could not generate a topology for your lipid (using ACPYPE/Antechamber), which may have several reasons.

  • The chemical geometry of the lipid is wrong. Therefore, first look at your lipid in a molecular viewer such as Pymol, Avogadro, or Rasmol. Does it look ok? Are some bond lengths wrong, that is, does the viewer draw all the expected bonds and no unexpected bonds? If there is an issue with the chemical geometry, you could try to optimize the geometry using, e.g., Avogadro (menu Extensions->Optimize Geometry).
  • The chemical valence of an atom is wrong. Are all expected hydrogen atoms present? Are the number of hydrogen atoms correct around double bonds? If hydrogen atoms are missing, you could add them with, e.g., Avogadro (menu Build->Add Hydrogens). For united-atom lipids, apolar hydrogens are of course not required.
  • Do you have a carbon atom with atom name 'CL' in your structure? This might be misinterpreted as chlorine, even if you have C in the element column of the PDB file (columns 77-78). Therefore, please replace the atom name CL by some other carbon-like name, such as CX, and resubmit. Then please replace the CX back to CL in the downloaded membrane patch, either using an editor (search and replace) or in a linux shell with 'sed s/CX/CL/ membrane.pdb > membrane_fixed.pdb.
If none if this helps, please contact us via e-mail, with the lipid file that caused the error as attachment.

System FAQs

  What are the system requirements for using MemGen?

The system should work on any computer or tablet which runs a modern web browser with JavaScript enabled.

  What file formats does MemGen work with?

The system will accept PDB, CRD, GRO, XYZ and MOL2 files as input, as long as each file does not exceed 1 MB or 500 atoms in length. The resulting membrane will be made available to you as a gzipped PDB file.

  How does the system handle files with multiple molecules?

For any uploaded structure file, MemGen will use only the first one.

  Can you provide a topology template to simplify further processing?

We don't provide topologies for download. If however you use GROMACS, you can use this shell script to generate a topology template.

  How does MemGen know the charge of a lipid?

MemGen uses the charge of a lipid to choose the number of counter ions. MemGen guesses the charge from a number of phosphate, sulphate, amine, and carboxyl groups. This procedure worked reliably for all common lipids we tested. If you notice that MemGen guesses the wrong charge for your lipid, please let us know.

  I don't know the Area per Lipid. What value should I use?

If in doubt, you may want to use the default value of 65 Å2 which is typical for phosphatidylcholine lipids. If the membrane happens to be unstable in an equilibration simulation, please try a larger area per lipid. Fortunately, MD simulations of membranes are quite stable, so your pressure coupling scheme will probably fix an incorrect area per lipid within a few nanoseconds.

  What is meant by the Area per Lipid if multiple lipid types are present?

MemGen places lipids on a square grid, composed of NxN square sites. The specified area per lipid determines the area of one such square site. Lipids with one or two tails are placed on one square site. Lipids with more tails use multiple sites (see image in the About section for an example).

  Can I add a membrane protein into the bilayer?

At present, MemGen does not allow the addition the proteins. However, because the lipids are highly ordered in the generated membrane, adding a protein to the box and removing lipids based on a simple overlap criterions yields a reasonable initial conformation for membrane protein simulations. For example, the Gromacs tool genbox does that if solute and solvent box provided to genbox have exactly the same unit cell.

  Can I build a liposome with MemGen?

Setting up liposomes is tricky due to the different areas between inner and outer leaflets. Because we don't know the equilibrium area per lipid, we see at present no reliable way to extend Memgen's functionality towards liposomes.

  Can I build an asymmetric membrane, with different lipid compositions in the inner and outer leaflet?

MemGen does not generate asymmetric bilayers with differing compositions of the two monolayers. The reason is that, because the areas per lipid are not additive in lipid mixtures, it is difficult to predict the equilibrated membrane area of some lipid mixtures. However, since membranes are nearly incompressible, any area mismatch between the two monolayers results in large lateral pressures. To set up such asymmetric membranes, we recommend to first equilibrate two symmetric systems, removing an appropriate number of lipids manually to achieve the same equilibrium area, and subsequently merge one leaflet from each simulation.

 

Depending on your options and file uploads, this may take several minutes.