[gmx-users] This may be it, but what to do?

[Marc Charendoff]

Here's what I've been able to do so far . . . 


1. Generated a  two molecule complex and saved as .pdb
2. Parsed the file out to retain relative coordinates
of each molecule in separate .pdb files
3. Run both resulting molecules through PRODRG server
to generate .gro files for GMX processing.
4. Merge molecules back together into a single complex
.gro file (again, hoping the coordinates are
preserved)
5. grompp resulting .gro for energy minimization run
6. run mdrun and watch my simulation explode

When I visualize my complex.gro file with VMD,
everything looks skewed (which now explains why my sim
didn't work). Any idea what happened? When I view the
PRODRG generated .pdb files, everything looks fine.
Did PRODRG somehow skew my .gro files? Any guidance
you could provide would be appreciated.

Regards, Marc