Thank you Prof. Lemkul, I appreciate your comment on this part.
Sir Peter Kroon, We want to do the coarse-grained MD simulation to access long timescale events of the effect of the ligand binding to the GPCR, at least microsecond . For now, the most accessible means for us is to do the CGMD. But we are currently being cornered in choosing which set-up will best suit, and if it will allow us to see these events. We are looking also in the possibility of coarse-graining the ligand, and if you can share your expertise in coarse-graining also the ligand that would be great. I appreciate this Sir Kroon, thank you very much! Best regards, Mac Kevin E. Braza On Mon, Apr 1, 2019 at 5:07 PM Peter Kroon <p.c.kr...@rug.nl> wrote: > If I may chip in: It really depends on what you're studying, and what > forcefield you're using to do it. Unfortunately there is no FF that > reproduces all behaviour accurately. The art is in picking one that (at > least) reproduces what you're interested in. > > > Peter > > On 29-03-19 17:26, Justin Lemkul wrote: > > > > > > On 3/29/19 9:17 AM, Mac Kevin Braza wrote: > >> 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 don't work with CG simulations, so I'm not much help. I would think > > that a CG parametrization of a ligand would remove all the detail > > you'd normally want to see in terms of ligand-protein interactions. > > > > -Justin > > > >> 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 <jalem...@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 > >>> > >>> jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org. > >>> > > > -- > 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. -- 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.
