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

[Mac Kevin Braza]

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.

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?

We will appreciate any help you will give. Thank you very much!

Best regards,
Mac Kevin E. Braza

On Fri, Mar 29, 2019 at 2:28 PM Mac Kevin Braza <mebraza at up.edu.ph> wrote:

> I am simulating a coarse-grained model of a octopamine receptor 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. I attached
> here the two files.
>
> 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/minco/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?
>
> We will appreciate any help you will give. Thank you very much!
>
> Best regards,
> Mac Kevin E. Braza
>