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?
Dear All Hi
You have to provide the topology file for your membrane which is POPC.
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?
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.