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 <[email protected]> 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 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 [email protected]. > -- 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 [email protected].
