As my first Gromacs simulation I am trying to simulate a protein with K+ ion. <br>When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and does not generate the topology file.<br><br>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?
<br><br>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?<br><br>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?<br><br><br>3. To insert the protein into a lipid I used genbox command:<br> genbox -cp protein.pdb -cs lipid.pdb<br><br>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?
<br><br>4. What is a better way of doing step 3? <br><br><br>Thanks<br><br>Mohamed Osman<br>Professor of Electrical Engineering<br>Washington State University<br> <br> <br>