[gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

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.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058