[gmx-users] Defining LA atoms in .gro file
bharat gupta
bharat.85.monu at gmail.com
Fri Apr 22 14:32:40 CEST 2016
On Fri, Apr 22, 2016 at 9:25 PM, Groenhof, Gerrit <ggroenh at gwdg.de> wrote:
> 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,
Thanks again for your prompt response. Yes,I have included the LA atoms
between the ligand and water molecules. Here's the file:
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
I am following your tutorial only and I have included the LA atoms same
way. So, where does this qmmm.itp file comes from ?? I included these LA
atoms to the .gro obtained from a snapstop of a simulation of my
protein-ligand complex.
Regards
BM
> >
> > 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.monu at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Defining LA atoms in .gro file
> > Message-ID:
> > <CAAh+zSV7BrctXYs0=
> > yoAekVnFbxeES+c0zTxODqA8jGin10ysQ at 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-request at 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list