[gmx-users] Problems with GROMPP

[Jens Pohl]

> It might be helpful to post to the list the exact commands you issued so far. 
> It might be illustrative of the problem.
> 
> -Justin
> 

Tried it with bash and tcsh.

pdb2gmx: -f *.pdb -o *.gro -p -q *.pdb -n -i opls-forcefield (no.6)

editconf: -f *.gro -o -bt cubic -d 0.1 -vol

genbox: -cp *.gro -cs (spc216-Water) -o -p

results in truncated protein (different sites of truncation)

I also tried different FFs with the same results. My protein is similar to 1MPY with only one chain to be simulated.

Jens 
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