[gmx-users] Lipid Bilayer Simulations

[Alan Dodd]

Configuring the .itp files etc initially is a bit
tricksy without knowing what you're doing, the short
not-very-helpful answer is "read the manual".  There's
a whole chapter (5?) on forcefield files and their
formats.
It's entirely possible to set it all up so that
pdb2gmx does in fact work, but to do this you need to
edit the forcefield files in the main gromacs folder
for these things (add your lipid.itp and dppc.itp, add
"#include" for each of these to your forcefield of
choice).  Anyways:  I'd guess it was complaining
initially because #include files were in the wrong
order in your .top, and then subsequently because you
removed the reference to lipid.itp (which you need). 
Unless someone can be of more help, I suggest you just
tinker.

--- toma0052 <toma0052 at umn.edu> wrote:

> Hi,
>      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.
> 
> Thanks,
> Mike Tomasini
> 
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