Hi Mike!
> 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
actually, in this way you are more or less editing your files and adding some solvent molecules, nothing
to do with FF & top/itp files related to lipid molecules ...
> 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
Mm, ok ... I think you have two different solutions you can try:
1. Download from the website of GROMACS
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,37/
a FF that is modified according to parameters describing lipids: I
personally have inserted in my
installation /usr/local/share/top (or whetheaver) directory these files and
everything is working fine
(both with 3.2 and 3.3 versions of GMX). In this way everything is included
in the default FF and path
in your machine. In case you do not have any access to your root directory
and you are not the machine
administrator, do not worry: insert all these untarred files in your working
dir and everything will
be fine! In this way you won'need any longer lipid.itp file for the used FF.
2. The second solution could simply be the usage of
#include "lipid.itp"
before
#include "dppc.itp"
in the topology file as suggested in the other reply.
> 'LC3' not found! As I
> said before, I am new to Gromacs, and I am not sure
That's the point ! Actually GROMACS does not know who this guy is ....
;)
Cheers and have nice MD on biomembranes
Luca
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