normal inserting transmembrane peptide in a bilayer

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13 years 5 months ago #423 by jmondal
I was planning to insert a martini KALP or WALP peptide inside a martini DPPC bilayer in a transmembrane manner. For that purpose, I was going through the MARTINI JCTC paper( vol.4 , page-819 ) introducing the protein force-field where a simulation study of KALP peptide in a bilayer has been discussed ( in page 828 of that paper) . But, I did not get any details how the KALP or WALP peptide are inserted in a bilayer as initial configuration.
So, I was wondering if I can get some help on how to insert this WALP peptide in to Martini DPPC bilayer . I guess, there may be some way of pulling , that may do the trick, but I am not sure how to keep it trans-membrane as well during pulling . So, Any suggestions will be helpful.

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13 years 5 months ago #424 by xavier
There are several way to do this:
1- simply adjust the position of your peptide using the gromacs tools (editconf/genconf ...) that the peptide would be at the right location in a pre-equilibrated bilayer. Then simply combine the two files ... that would generate a file that you can visualize with for instance vmd. Working with pdb files helps not to have to adjust the number of particules ...
Then you can try a simple minimuzation, it might be sufficient. However removing the overlapping lipid would certainly be helpful.

2- use a gro file format for both the lipid and peptide conformations. Then after placing the peptide a reasonable location (as previously) define the box size in the gro file as exactly the same as the one for the preformed bilayer. Then use genbox giving the bilayer conformation to -cs option and the peptide file to -cp option. Play with the option -vdwr to get the right solvation of your system.

Either solution would work.

You can also look at the few tutorials existing for atomistic simulations and adapt them to the CG ... it is pretty easy and would be a great exercise if your are not familiar with these tools.

XAvier.

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