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

[Justin Lemkul]

On 3/18/15 4:05 PM, Thomas Lipscomb wrote:
> 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
>

I have no idea why this works.

> 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.

Topologies are not coordinates.  You need to actually construct the system 
correctly.  If you have only DPPC, then you don't have a protein, which means 
you've probably forgotten to do something.

-Justin

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

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

==================================================