When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and does not generate the topology file.
When I remove the K+ ion, I get a topology file, but I need the K+ for the simulation. Can I add the K+ ions at the end of the .gro files and proceed?
1. How can I run pdb2gmx and tell it to look for the force filed information for K in a different file? I tried -ff but got unclear message?
2. When I searched in the share/top directrory I found that each force field name with several extensions:.itp, .dhb and .atp. I only have a K.itp file, is that enough?
3. To insert the protein into a lipid I used genbox command:
genbox -cp protein.pdb -cs lipid.pdb
The protein sinks deep into the lipid and I need to shift the protein back up? What is the best to do it without overlapping with the solvent molecules?
4. What is a better way of doing step 3?
Thanks
Mohamed Osman
Professor of Electrical Engineering
Washington State University
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