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

[Thomas Lipscomb]

Dear gmx-users,
I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the CHARMM36 forcefield.  I think the lipid shrinking was a step I did badly last time (I think I was getting "can open em.tpr but not open em1.tpr, em2.tpr, etc."), which might be why that run had poor lipid packing.
This is the page of the tutorial I am stuck at:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The KALP15 in DPPC tutorial says to scale down the lipids by 0.95 for 26 times.  So I repeated this group of 3 commands 26 times:/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 -vperl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
I am not sure what file to check to make sure doing that is right.  I hope it is.
Anyway I also tried:
cp em.tpr em1.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tpr/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -vperl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.datcp em1.tpr em2.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p topol.top -o em2.tpr/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -vperl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.datcp em2.tpr em3.tpr
etc.
But then I got this error I have never seen before:-------------------------------------------------------
Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311
Fatal error:Topology include file "gb.itp" not foundFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------
Line 311 is the contents of this if statement

    if (!cpp->fn)    {        gmx_fatal(FARGS, "Topology include file \"%s\" not found", filenm);    }
Sincerely,Thomas