[gmx-users] Lipid Bilayer Simulations

toma0052 toma0052 at umn.edu
Fri Sep 29 03:11:58 CEST 2006

     I am new to Gromacs, and I am working with lipid bilayer simulations. 
I am attempting to just run an energy minimization on a lipid bilayer so I
can get a better feel for the program.  I have taken the files dppc128.pdb,
dppc.itp, lipid.itp and example2.itp from Peter Tieleman's website. 
Because I could not use teh pdb2gmx command, I started with the editconf
command and then the genbox command, both of which seemed to run
successfully.  Then, I tried to do the preprocessing with the grompp
command, but I received the error; Fatal Error: Found a second defaults
directive, file "lipid.itp".  When I removed lipid.itp from the topology
file, I received the error; Fatal Error: Atomtype 'LC3' not found!  As I
said before, I am new to Gromacs, and I am not sure how to get around this
problem. Do I need to put the dppc.itp and lipid.itp file together into
one?  Any help would be appreciated.

Mike Tomasini

More information about the gromacs.org_gmx-users mailing list