[gmx-users] KALP15 in DPPC tutorial: system_shrink1.gro error?

[Thomas Lipscomb]

Dear gmx-users:
Following this tutorial, using Maximin 3 instead of KALP15 and charmm36 instead of gromos53a6:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html


When I do this:

/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em.tpr

/usr/local/gromacs/bin/gmx mdrun -s em.tpr -v

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

I get the error:
Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/fileio/futil.cpp, line: 545
File input/output error:system_shrink1.gro

and later another error:
Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603
Fatal error:number of coordinates in coordinate file (system_shrink1.gro, 6400)             does not match topology (topol.top, 17617)

system_shrink1.gro contains all 128 DPPC lipids (6400 atoms) that I started with but somehow does not include the maximin 3 protein nor the water solvent.
In the tutorial:"Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. "
Now there were 128 lipidswith 50 atoms per lipidThere are 3 lipids within cut-off range...1 will be removed from the upper leaflet...2 will be removed from the lower leaflet..

3 cut off lipids * 50 atoms each = 150 and the original number of atoms was 17606, so 17606 - 150 = 17617 (which is the topol.top number from the error).  So the topol.top appears correct.

system_shrink1.gro is exactly the same as my previous run of the tutorial that worked so system_shrink1.gro is not the problem?  Then why did it have a File input/output error?

Do I fix the topol.top?  That is the file has different numbers (eg in [ angles ]) than my previous run (because I used a different forcefield?).

Sincerely,Thomas