[gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow

Thomas Lipscomb linuxborg2 at yahoo.com
Fri Feb 13 05:24:05 CET 2015

Dear gmx-users,
I am following the KALP tutorial below:KALP-15 in DPPC Tutorial progress point

At this step I get this error (and I know that the discrepancy is because the 23 DPPC molecules are not included):
/usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr

Fatal error:number of coordinates in coordinate file (model1_solv.gro, 12266)             does not match topology (topol.top, 11116)

For more information, see my Folder with all of my KALP Tutorial files
  I see that trying to #include "dppc.itp" is not the right way to go because it has the same precedence as forcefield.itp.
So my guess as to what is wrong is that I messed up the contents of the gromos53a6_lipid.ff folder somehow when I was making them in "Step Two" of the tutorial.
This seems to say that the problem is probably with these two files in the gromos53a6_lipid.ff folder: ffnonbonded.itp and ffbonded.itphttp://comments.gmane.org/gmane.science.biology.gromacs.user/50436
So how do I (manually?) fix the ffnonbonded.itp and ffbonded.itp files?  Or did I miss a step in the tutorial?  I could redo the tutorial (up to my progress point) pretty quickly.

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