[gmx-users] Coarse-grained Protein-ligand simulations

Justin Lemkul jalemkul at vt.edu
Fri Mar 29 13:58:28 CET 2019

On 3/29/19 3:32 AM, Mac Kevin Braza wrote:
> Hello everyone,
> I am simulating a coarse-grained model of a membrane protein (GPCR) in
> lipid bilayer and an all-atom ligand octopamine. I build the protein,
> solutes, and membrane in the web server CHARMM-GUI. While, I added the
> ligand to the protein complex manually using the same coordinates of the
> coarse-grained protein model.
> I used the GROMACS input files from the output of CHARMM-GUI to simulate
> the system. I include the LIGAND.ITP (from the PRODRG Server) to the
> system.top and added the atom indexes in the index.ndx file.

Don't do this. An atomistic representation of a ligand and a CG 
representation of everything else is incompatible. Mixing and matching 
force fields is never a good idea. Moreover, PRODRG produces topologies 
that are known to be unsuitable for MD simulations.

> However, when I proceed with the second part of equilibration, the
> following errors occurred.
> *Command line*:
>    gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -c
> step6.1_equilibration.gro -p system.top -n index.ndx
> Setting the LD random seed to 1722366284
> Generated 2391 of the 4656 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'PROA_P'
> Excluding 1 bonded neighbours molecule type 'POPC'
> Excluding 1 bonded neighbours molecule type 'W'
> Excluding 1 bonded neighbours molecule type 'NA'
> Excluding 1 bonded neighbours molecule type 'CL'
> Excluding 3 bonded neighbours molecule type 'LIG'
> Velocities were taken from a Maxwell distribution at 303.15 K
> Removing all charge groups because cutoff-scheme=Verlet
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.4
> Source code file: /home/gromacs-5.1.4/src/gromacs/gmxpreprocess/readir.c,
> line: 2690
> Fatal error:
> 20 atoms are not part of any of the T-Coupling groups
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> The 20 atoms described the ligand I placed inside the protein-membrane
> complex. I want to know if where can this error originate and how can we
> fix them?

This simply means you haven't specified the ligand anywhere in tc-grps. 
But again, back up and reevaluate your approach, which is far more 
problematic than this simple index group issue.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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