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bjoern
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Tutorial: Import and work with custom lipid PDBs in CmME

Post by bjoern » 11.05.2017, 09:27

CmME comes already with a number of lipid files. If you want to create a membrane for illustrative purposes, then it is normally sufficient to use the delivered lipid files. But, in case you want to prepare a simulation, e.g. with GROMACS, you will usually want to use your own files, as you need PDB files which are compatible with the corresponding topology.

Or, let us say you have a lipid file which you want to use, but it is in an uncomfortable state for packing. For example, you generated a PDB file based on a MOL file and the structure is not minimized - resulting in a very bad packing. I will use here as a very good "bad" example the file DLPm which is also coming with CmME.

Here I will explain how you can
  • open the file in Jmol starting from CmME
  • modify the file with Jmol
  • re-import it to CmME
  • start a membrane packing algorithm with this file

Click on the green folder in the LIPIDS category and import your custom lipid file or use a file already found in the database of CmME.
1_lipid_import_local_db.png
1_lipid_import_local_db.png (26.83 KiB) Viewed 6644 times
For hints where to find custom lipid files, please have a look here:

http://www.cellmicrocosmos.org/Cmforum/ ... p?f=9&t=20

But of course it is important that you use a lipid with the corresponding topologies. Maybe have a look to the Gromacs download section, if the right files are provided.

For the MembraneEditor side, it is easy, you just need the correct PDB file. It will export than an All-Atom membrane.

If you have a lipid PDB which is not in a good configuration, use Jmol. Open the file in Jmol (you can do it from the MembraneEditor, if you put a single lipid on the membrane - just drag'n'drop from the lipid entry in the Default area onto the membrane area. Just do it with a single one. I use here the file DLPm which is delivered with the CmME - but you can use your imported custom file instead of this.
2_lipid_import_DLPm.png
2_lipid_import_DLPm.png (78.2 KiB) Viewed 6644 times
Open in Jmol
3_lipid_import_JMOL_button.png
3_lipid_import_JMOL_button.png (5.03 KiB) Viewed 6644 times
4_lipid_import_JMOL_DLPm.png
4_lipid_import_JMOL_DLPm.png (93.75 KiB) Viewed 6644 times
Open the model kit - this is a very nice feature of Jmol which you can use to minimize the structure in a very simple way:
5_lipid_import_JMOL_model_kit_button.png
5_lipid_import_JMOL_model_kit_button.png (5.62 KiB) Viewed 6644 times
Select:
6_lipid_import_JMOL_model_kit_menu.png
6_lipid_import_JMOL_model_kit_menu.png (64.13 KiB) Viewed 6644 times
Select single atoms and move them to the preferred position and repeat it several times until you achieved a good state:
7_lipid_import_JMOL_DLPm_mod.png
7_lipid_import_JMOL_DLPm_mod.png (95.51 KiB) Viewed 6644 times
Change to normal movement mode/exit the model kit mode, right click on the background, and save the file like this:

Open the console:
8_lipid_import_JMOL_open_console.png
8_lipid_import_JMOL_open_console.png (58.64 KiB) Viewed 6644 times
Then:
9_lipid_import_JMOL_console.png
9_lipid_import_JMOL_console.png (41.06 KiB) Viewed 6644 times
Re-import it to the MembraneEditor like you are used to:
10_lipid_import_reimport.png
10_lipid_import_reimport.png (26.83 KiB) Viewed 6644 times
11_lipid_import_reimported.png
11_lipid_import_reimported.png (165.05 KiB) Viewed 6644 times
(Here you can see, it is a good idea to give the PDB file a better name, a short code like the original file. So I recommend to start with a 4-letter code and do not follow the bad idea given by this image to use a long name.)

Now use for example the Distributor algorithm to generate the memrbane. Use all options of the first window, then type in the required area per lipid, like this:
12_lipid_import_start_mpa_distributor.png
12_lipid_import_start_mpa_distributor.png (333.28 KiB) Viewed 6644 times
Then hit "Apply Counts"! If the desired APL is not reached after a longer time waiting, optimize the PDB file again with Jmol. As a rule of thumb: if ca. 80% of APL are reached within the first 2 minutes (e.g., on my Mac Book Pro from 2015), you can wait for a longer time (30 min) if the remaining 20% are reached or not.

Done!

Have fun!
Bjorn

P.S.: Also the MembraneEditor is coming with a build-in editor to modify the lipid files. But here, no minimization is implemented. However, this feature is interesting if you want to create multiple conformation based on a single PDB file. More info here:
https://www.cellmicrocosmos.org/index.p ... /7-1-about

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