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

[Justin Lemkul]

On 3/17/15 12:12 AM, Thomas Lipscomb wrote:
> 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.

Visualizing is a start.  Are the lipids becoming more compact around the 
proteins?  It should be very easy to tell.

> 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-------------------------------------------------------

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

> Line 311 is the contents of this if statement
>
>      if (!cpp->fn)    {        gmx_fatal(FARGS, "Topology include file \"%s\" not found", filenm);    }
> Sincerely,Thomas
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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