Membrane simulation


#1

Dear All Hi
I am working on a membrane protein. I created a membrane using VMD “membrane builder” and merged it with the protein pdb file by “Merge Structures” of VMD, for the rest of works I tried to use gromacs. My idea is to modify gromos53a6 and such that creates the protein-membrane complex topology file. I used the following tutorial:
KALP-15 in DPPC - Bevan Lab - Virginia …
But when I run pub2gmx command, the following error is appeared:
Residue POPC not found in residue topology database.
Do you have any idea?


#2

You have to provide the topology file for your membrane which is POPC.


#3

thank you scinikhil
But, I think, to this aim the lipid.rtp file is needed and I can not find it for gromos53a6 which the tytorial is based on.
fortunatly, I found lipids-AMBER-POPC-joakim-v2 pakage that contains all necessary files for lipids such as lipid.rtp, atomtypes.atp, forcefield.itp and fnonbonded.itp. so I combined this files with the corresponding files in the amber99sb-ildn force fileds and run the md as a normal method using this new forcefield.
every thing sounds good.
I would like to know is it right? Are have the same experience?


#4

Hi,
you can think to use BiKi Life Sciences to build your membrane-protein easily. Have look to www.bikitech.com
If you need an academia license you can contact me in private.
Best
and