So I found out why I didn't use charmm-gui initially, when using the protein membrane builder it removes the ligand minocycline. I have found a solution, on the unlikely chance what I have done will help someone, I'm going to post what I did.
Since I used transformations on the protein (aligning to z axis, moving along z axis) it made it difficult to align minocycline with the charmm-gui protein as well as needing to fix hypervalent carbons. I first aligned the xtal and charmm-gui proteins with uscf chimera. Then outputted the minocycline coords and fixed the bonds with Spartan '08. Then I used charmm-gui Ligand Reader & Modeler to output charmm36.itp and MIY.itp. I renamed charmm36.itp to charmm36_2.itp and added both to the charmm-gui directory and included them in .top. I combined the two pdbs (protein/lipids/water and minicycline) and removed any TER/END's in the middle. I also added minocycline to index.ndx. Thanks for the help! - Jonathan On Mon, Mar 13, 2017 at 9:24 PM, Jonathan Saboury <[email protected]> wrote: > I honestly forgot why (took too long, erred, or both) so I tried to do > charm-gui again. From my current attempt it is taking a while. I'm on the > last step and I'll keep checking the output. > > I'll keep you updated when something happens. > > Thanks again, your help is invaluable! > > - Jonathan > > P.S. I am seriously impressed on all the projects you are on and still > have time to do user help XD > > On Sun, Mar 12, 2017 at 5:59 PM, Justin Lemkul <[email protected]> wrote: > >> >> >> On 3/12/17 8:36 PM, Jonathan Saboury wrote: >> >>> Hello all, >>> >>> I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the >>> minimization, >>> equilibration, and production runs given. Then I copied the 10ns >>> production >>> run .gro to a different folder so that I can run it with >>> charmm36-nov2016.ff instead of the ff given. >>> >>> >> Why? The topology CHARMM-GUI gives you still works, and that's sort of >> the purpose - it gives you everything you need for the system. >> >> When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f >>> old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top >>> -water >>> tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ] >>> and >>> perhaps other headings. >>> >>> I was under the impression that the .top should have been small and just >>> contained the include line for where the POPE and POPG .itps were in the >>> charmm36-nov2016. Did I do something wrong? Would this give me a >>> simulation >>> that isn't accurate? >>> >>> >> No, because pdb2gmx will generate an explicit copy of the topology for >> every instance of every residue, which leads to an extremely redundant >> topology with many copies of lipids and water. As stated above, there is >> no need to re-generate your topology. Use what CHARMM-GUI gives you. We >> worked hard to make it easy for the end user :) >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> [email protected] | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> 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].
