Hello everyone,
I have downloaded the POPC128.pdb from http://wcm.ucalgary.ca/tieleman/downloads. As 128 lipid molecules are not enough for my receptor (GPCR) I am supposed to increase the number of lipids. Any suggestion on how to replicate the lipid molecules.
Thanks in advance
Use genconf -nbox to replicate the membrane patch along x and y.
Make sure to make molecules whole before you do so.
Thank you justin. I have used genconf module with box vectors 2 1 1 and generate the other membrane patch. but i am confused with "make molecules whole" in your previous comment. Can you please clarify me
Thanks.
Not relevant here, actually. The POPC molecules are intact. Compact representations in which all atoms have been put "inside" the box can "break" molecules, making replication in this manner incorrect. It's just a periodicity thing. Always make sure molecules are whole (visual inspection) and if they aren't, make them whole with trjconv.
Hi Justin,
I wanted to make a 512 lipid bilayer from the 128 lipid bilayer model. As you mentioned I put the lipid whole in the 128 lipid model with trajconv -pbc whole and it doesnt have any breaking bond, but when I used genconf -nbox 2 2 1 and visualized with VMD, we see a lots of drawing lines between lipids. whats wrong with this?
Without a snapshot of it or the coordinate file itself, there's nothing I can really tell. But if you properly made the molecules whole, there should be no PBC issues.
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