[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119
bharat gupta
bharat.85.monu at gmail.com
Fri Apr 22 09:07:08 CEST 2016
On Thu, Apr 21, 2016 at 7:12 PM, Groenhof, Gerrit <ggroenh at gwdg.de> wrote:
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> 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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