> As my first Gromacs simulation I am trying to simulate a protein with K+ > ion. > 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?
No that won't work. You need to choose a force field that has been parameterized to include your protein and your ion. I don't know if this one has. > 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? You can use the #include mechanism in your .top if you have an .itp file for potassium. > 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.itpfile, is that enough? Yes, if it's complete. Have a read of chapter five of the manual. > 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? Start with MD on a simple system while you work out how things work. First just your protein. Then with the ion. Then worry about the lipid. > 4. What is a better way of doing step 3? I don't know. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php