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

[Mac Kevin Braza]

Thank you Professor Lemkul,

But would you suggest on how can I coarse-grained the ligand I am using? I
have been searching resources online but they do not work in our part.

I hope you can help us. Thank you Prof. Lemkul!

Best regards,
Mac Kevin E. Braza

On Fri, Mar 29, 2019, 8:59 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
> ==================================================
>
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