[gmx-users] Martini and Gromacs 3 and 4

[Steve]

Hi Tsjerk
Thanks for you response. Yes, that is exactly what I was confused about.
I am presently attempting to  use "initram.sh". However, I keep getting the
following error :

Now executing...

./initram.sh -f confout.gro -p systemFG.top

Checking dependencies:
backward.py ... /home/stevesei/bin/backward.py
grompp ... /home/stevesei/bin/grompp
mdrun ... /home/stevesei/bin/mdrun
Residues defined for transformation from martini to gromos54a7:
[]
Traceback (most recent call last):
  File "/home/stevesei/Downloads/backward/backward.py", line 821, in
<module>
    raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: ALA



Therefore, I must have my "Mapping" directory in the wrong location?? I
placed it in both the working directory and in /home/stevesei/bin but I keep
getting the above message.

I would appreciate any help..thanks much, Steve

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