Why should we delete all the water from protein surface. Actually i am doing this in simulation in a urea box. How do i remove water from protein surface?
On Tue, Sep 11, 2018, 10:19 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Then I think we need to delete all the waters from protein surface > > On Tue, Sep 11, 2018 at 10:06 AM, ISHRAT JAHAN <jishra...@gmail.com> > wrote: > > > I am getting the same error as u have posted today. Segmentation fault > core > > dumped. Although my minimization runs properly. > > > > On Mon, Sep 10, 2018, 6:30 PM Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in> > > wrote: > > > > > You upload the warning given by mdrun. I think there is a problem with > > the > > > initial configuration of your .pdb file. Please upload all the lines > > > written in your terminal during mdrun operation > > > > > > On Mon, Sep 10, 2018, 4:13 PM ISHRAT JAHAN <jishra...@gmail.com> > wrote: > > > > > > > Thank u for your reply sir. I have changed the -Dflexible to -DPosres > > but > > > > still gets the same problem. > > > > > > > > On Mon, Sep 10, 2018 at 3:24 PM Bratin Kumar Das < > > > > 177cy500.bra...@nitk.edu.in> wrote: > > > > > > > > > I think you should remove define=-DFLEXIBLE > > > > > and define=-DPOSRES in the .mdp file. Give 1000 force constant. > Don't > > > > > give large force costant. > > > > > > > > > > On Mon, Sep 10, 2018, 3:14 PM ISHRAT JAHAN <jishra...@gmail.com> > > > wrote: > > > > > > > > > > > Dear all, > > > > > > I am trying to do energy minimization of two docked protein. At > the > > > > > energy > > > > > > minimization step during MD simulation process, the em.gro file > is > > > > found > > > > > to > > > > > > be broken due to which equilibration of protein does not occur > and > > > core > > > > > > dumped error has been found. > > > > > > Please help me in this regard. I am attaching my em.mdp file and > > > > snapshot > > > > > > of em.gro file. > > > > > > ; Lines starting with ';' ARE COMMENTS > > > > > > ; Everything following ';' is also comment > > > > > > > > > > > > title = Energy Minimization ; Title of run > > > > > > > > > > > > ; The following line tell the program the standard locations > where > > to > > > > > find > > > > > > certain files > > > > > > cpp = /lib/cpp ; Preprocessor > > > > > > > > > > > > ; Define can be used to control processes > > > > > > define = -DFLEXIBLE > > > > > > > > > > > > ; Parameters describing what to do, when to stop and what to save > > > > > > integrator = steep ; Algorithm (steep = steepest > > descent > > > > > > minimization) > > > > > > emtol = 1000.0 ; Stop minimization when > > the > > > > > > maximum force < 1.0 kJ/mol > > > > > > nsteps = 2000 ; Maximum number of > (minimization) > > > > steps > > > > > to > > > > > > perform > > > > > > nstenergy = 1 ; Write energies to disk every > > > > nstenergy > > > > > > steps > > > > > > energygrps = system ; Which energy group(s) to write > to > > > > disk > > > > > > > > > > > > ; Parameters describing how to find the neighbors of each atom > and > > > how > > > > to > > > > > > calculate the interactions > > > > > > ns_type = grid ; Method to determine neighbor list > > (simple, > > > > > grid) > > > > > > coulombtype = PME ; Longrange electrostatics > (Ewald) > > > > > > rvdw = 1.0 > > > > > > rlist = 1.0 > > > > > > rcoulomb = 1.0 > > > > > > fourierspacing = 0.12 > > > > > > pme_order = 4 > > > > > > ewald_rtol = 1e-5 > > > > > > constraints = none ; Bond types to replace by > > > constraints > > > > > > pbc = xyz ; Periodic Boundary Conditions > > > (yes/no) > > > > > > [image: Screenshot_from_2018-09-10_14_59_11.jpg] > > > > > > > > > > > > -- > > > > > > Ishrat Jahan > > > > > > Research Scholar > > > > > > Department Of Chemistry > > > > > > A.M.U Aligarh > > > > > > -- > > > > > > 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. > > > > > > > > > > > > > > > > > -- > > > > Ishrat Jahan > > > > Research Scholar > > > > Department Of Chemistry > > > > A.M.U Aligarh > > > > -- > > > > 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. > > > -- > 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.