[gmx-users] Defining LA atoms in .gro file
Groenhof, Gerrit
ggroenh at gwdg.de
Fri Apr 22 14:25:56 CEST 2016
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.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
>
> --
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