Hi again, >From the error message it seems that the virtual_sites are not in the same >topology file. Since introduction of molecular topologies in GMX4, all QM >atoms must be in the same topology entry. It appears that in your case there >is a stretch of atoms, perhaps waters, in between the link atoms and the atom >group containing the QM atoms. This seems bit cryptic perhaps, but include the >link atoms in your qmmm.itp file.
In gromacs 3, on which the tutorial was based, this was not a problem yet. Best, Gerrit > > Hi, > > Indeed, Link atoms have to be added to the .gro file. The atom indexing in > the .gro file is not used, so no need to renumber. A simple editconf can do > that for you if too, if you would like to have the numbering correct. > However, you need to adjust the total number of atoms at the top of the > .gro file. > > for the bonded interactions, you should remove the gb_x , because these > defines contain the bond type information as well. Easiest is to add a ';' > like this > > 1851 1853 2 ; gb_10 > > which means that what comes after is ignored. > > good luck, > > Gerrit > Hi Gerrit, Thank you for your previous response to my queries. I made the changes according to your suggestion and I got the following error while running the grompp command: $ gmx grompp -f qmmm1.mdp -c start.gro -n QM_MM.ndx -p topol.top -o qmmm1.tpr WARNING 1 [file qmmm1.mdp, line 62]: Unknown left-hand 'continuation' in parameter file Setting the LD random seed to 1943711519 Generated 189 of the 2080 non-bonded parameter combinations ------------------------------------------------------- Program gmx grompp, VERSION 5.1.2 Source code file: /home/Bharat/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line: 1806 Fatal error: [ file topol.top, line 22177 ]: Atom index (3563) in virtual_sites2 out of bounds (1-3496). This probably means that you have inserted topology section "virtual_sites2" in a part belonging to a different molecule than you intended to. In that case move the "virtual_sites2" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I have included the LA atoms in the topology file under the section name [dummies2]. Here's my qmmm1.mdp file: title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein 5YWR ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy unconstrained_start = no Shake-SOR = no shake_tol = 0.0001 lincs_warnangle = 30 morse = no ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_5YWR Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no gen_temp = 00 gen_seed = 18111976 QMMM = yes QMMM-grps = Protein_AS_5YWR QMmethod = am1 QMMMscheme = normal QMbasis = sto-3g QMcharge = 0 QMmult = 1 the QM parameters were copied from a tutorial ( http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html) to test the trial run. I am using ORCA for QMMM calculations. Could you please let me know how to rectify these errors. Regards BM > > Message: 3 > Date: Thu, 21 Apr 2016 17:43:47 +0900 > From: bharat gupta <bharat.85.m...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] Defining LA atoms in .gro file > Message-ID: > <CAAh+zSV7BrctXYs0= > yoaekvnfbxees+c0ztxodqa8jgin10...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear GMX Users, > > I am trying to perform QM/MM simulation for my system and I need to define > LA for the boundary between QM and MM region. I have the boundary regions > but I don't know how to add them in the gro file. Do I have to manually > modify the .gro file, if that's the case, adding, them manually how do I > renumber the rest of the atoms and residues? Here's what I have done: > > 3715YWR H21 3562 4.283 4.647 4.755 -1.1354 1.0843 -0.8713 > 372XXX LA 3563 2.475 3.856 2.040 -0.0020 -0.1066 0.1995 > 373XXX LA 3564 0.475 3.856 2.040 -0.0020 -0.1066 0.1995 > 374XXX LA 3565 1.475 3.856 2.040 -0.0020 -0.1066 0.1995 > 375XXX LA 3566 3.475 3.856 2.040 -0.0020 -0.1066 0.1995 > 376XXX LA 3567 0.875 3.856 2.040 -0.0020 -0.1066 0.1995 > 377XXX LA 3568 1.575 3.856 2.040 -0.0020 -0.1066 0.1995 > 372SOL OW 3563 3.414 3.445 2.243 -0.1786 -0.5561 0.4692 > 372SOL HW1 3564 3.479 3.440 2.167 0.5613 -1.1084 1.1215 > 372SOL HW2 3565 3.329 3.488 2.212 0.4389 0.0440 -0.4374 > 373SOL OW 3566 1.589 3.334 2.348 0.6300 0.1793 -0.1279 > 373SOL HW1 3567 1.639 3.413 2.384 1.2205 0.0166 -0.5746 > 373SOL HW2 3568 1.588 3.337 2.248 -1.5585 0.9770 -0.1508 > 374SOL OW 3569 5.280 6.227 4.070 0.5862 -0.1571 -0.6930 > > So, I added the LA atoms between atom no H21/3562 and OW/3563 manually. > Please let me whether this is the correct way of adding the LA atoms ? > > Also, I need to modify the bond_types as well in the topology file to 5. Is > this the correct way: > > 1851 1853 2 gb_10 > 1853 1854 5 gb_2 > 1853 1855 5 gb_21 > 1855 1856 5 gb_27 > 1855 1862 5 gb_27 > 1856 1857 5 gb_27 > 1857 1858 5 gb_27 > 1858 1859 5 gb_5 > 1858 1860 5 gb_13 > 1860 1861 5 gb_1 > 1862 1863 5 gb_5 > 1862 1864 2 gb_10 > 1864 1865 2 gb_2 > > I haven't changed the values for C0 for the QM atoms but I have changed > their type to 5. > > -- > *Best Regards* > BM > > -- > 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.