[gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)

[Thomas Lipscomb]

Dear gmx-users,
"This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails.  If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs.
-Justin"

Thanks.  Strangely, charmm36.ff already had gb.itp, but what fixed that file not found error that was copying all of the files (including gb.itp) from:
/usr/local/gromacs/share/gromacs/top/charmm36.ff

to my working directory:
/home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP/charmm36_lipid.ff

While not overwriting the modified files that were already in charmm36_lipid.ff

But now I am getting the 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, 6802)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------

topol.top has this:
[ molecules ]; Compound        #molsProtein_chain_A     1DPPC              128

But the system_shrink1.gro only has the DPPC not the protein.  The protein has 402 coordinates so clearly system_shrink1.gro not having the 402 protein coordinates is the problem.
Do I copy the 402 protein coordinates from [ atoms ] in topol.top to system_shrink1.gro?  The coordinates seem to be in different formats.
Sincerely,Thomas