Here's a little page about how
I got Gromacs working
Gromacs
is a program for the purpose of doing molecular dynamics:
The manual is quit extensive and everything is clearly explained. You
can download it from
http://www.gromacs.org
I made in my Home/Programs/
a directory gromacs
Herein I downloaded the gromacs package; unpacked it..
This generated a new directory : gromacs3.1
(or whatever the version was)
Then I had to make sure the PATH was ok: in my case gromacs was in the
/usr/local/gromacs/i686-pc-linux-gnu/bin
so I corrected my path is the .bashprofile
:
export
PATH=/usr/local/gromacs/i686-pc-linux-gnu/bin:${PATH}
Most of the information for beginners can
be found in the "getting
started" part
This is usually in the share/html
directory
According to the instructions I started with converting pdb2gmx.
The PDB-file I used was 1TOH.pdb . However, after running this program,
I didn't find all the files I had to find: topol.top (present),
conf.gro (absent). So, I checked the console and it said :
" residue FE not
found in the residue topology database "
Since "FE" is also known as "Iron", I figured it could have been due to
this. In my case it was present because it had been used for
crystallization of the protein. Anyway, I therefore edited the pdb-file
by removing the links to iron: see the 1TOH page, which
solved the problem, generating the desired conf.gro file as well.
It is a good choice to first run some demos and examples before
actually starting.. however,
For the impatient ones amongst you, there's a very nice website : Introduction to
molecular modeling which should give you the basics on the program
and help you run the simulations.
