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 <mebr...@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 > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.