[gmx-users] Martini and Gromacs 3 and 4

[Tsjerk Wassenaar]

Hi Steve,

Try using -to gromos
The definitions are not (yet) explicitly set for each flavour of gromos.

Cheers,

Tsjerk


On Tue, Nov 26, 2013 at 6:01 PM, Steve <stevesei at ymail.com> wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.