I am really struggling to give inputs in http://www.charmm-gui.org/?doc=input/membrane_only&step=1 for generating the lipid parameters for POPC compatible with CHARMM 36 force field as in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html for DPPC.
Dear Roshan
Hope, you will find parameters in the following link: https://lipidbook.bioch.ox.ac.uk/package/allpackages.html
Thanks Jamoliddin, but couldnot find the one for POPC for CHARMM 36 forcefield.
Check out this one: http://bioinf.modares.ac.ir/software/mb2/download.php
The CHARMM-GUI webserver already has the POPC topology and parameters. In the step where you define the membrane (the page you give) you simply need to define the dimensions of your membrane and its compositions (either as percentage ratios or as actual number of lipids). After you're done with all the steps, the server will give you a tgz file with everything you need, including the parameter files.
See the picture I attached to understand what I'm talking about:
Thanks Fotis, I actually did just like you told to generate POPC membrane using CHARMM-GUI. Thanks one again.
- Badges
- Science topic