[gmx-users] pdb2gmx with force field option

[Mohamed Osman]

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?


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.itpfile, 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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