Hey everyone,
I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with
gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp
I get hit with this error:
Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
does not match topology (topol.top, 6438)
I figured that since my number of molecules were off that the problem was either the way I updated the molecules section of my topol.top fill by adding
DPPC 126
after seeing this when adding lipids:
There are 128 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet
Centering protein....
Checking for overlap....
...this might actually take a while....
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...
But for some reason I can't seem to start the EM iterations because of this error.
Its the frequent error in MD simulation, you need to append the DPPC molecule from .top in .gro file and make manual corrections in .gro file about the number of solvent molecules, DPPC molecule and solute (NA or CL)
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