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Fatal error:
Atom 'HO2 in residue DG 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.
Fatal error: Atom 'HO2 in residue DG 1 was not found in rtp entry DG5 with 31 atoms while sorting at
A 'HO2 atom in DG (DNA guanosine) is strange, both the naming convention ('H…) and the hydroxyl are non-typical for a DNA residue. Check your PDB atom naming against the .rtp file (it should be mentioned in the error message, sth like /usr/share/gromacs/top/amber99bsc1.ff/dna.rtp depending on your installation). If all the heavy atoms are named correctly, and no further errors are there, you can use -ignh in pdb2gmx to generate hydrogens from scratch instead of relying on perhaps incorrectly named existing ones.
Thank you for the swift response. I actually converted the RNA molecules to DNA using pymol by selecting and altering the residues followed by, remove name O2P+O2 for the hydroxyl. Previously I’d tried ignoring hydrogen but gets fatal error at the stage of adding charges. I will reconfirm the PDB atom naming against the .rtp file.
Analysing residue names:
There are: 31 DNA residues
There are: 1680 Water residues
Number of degrees of freedom in T-Coupling group rest is 12987.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 24x44x44, spacing 0.101 0.115 0.115
Estimate for the relative computational load of the PME mesh part: 0.26
This run will generate roughly 1 Mb of data
There were 2 notes
There was 1 warning
Program: gmx grompp, version 2020-rc1-MODIFIED
Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 2352)
Thanks for the suggestions. it did help. However, I am finding it difficult to use the -maxwarn command. it is showing the errors below: -
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Error in user input:
Invalid command-line options
In command-line option -maxwarn
Too few (valid) values
-maxwarn has to go with an integer value, will be -maxwarn 1 in your case to ignore a maximum of 1 warning.
Thank you very much
At the energy minimization stage it is showing me this error
Program: gmx mdrun, version 2020-rc1-MODIFIED
Source file: src\gromacs\domdec\domdec.cpp (line 2275)
MPI rank: 0 (out of 24)
Fatal error:
There is no domain decomposition for 18 ranks that is compatible with the
given box and a minimum cell size of 2.83813 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
The em log
Input Parameters:
integrator = steep
tinit = 0
dt = 0.001
nsteps = 50000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -1159719968
emtol = 1000
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 0
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 1
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 40
fourier-ny = 60
fourier-nz = 60
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
tcoupl = No
nsttcouple = -1
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = false
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = false
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = false
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
simulated-tempering = false
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
applied-forces:
electric-field:
x:
E0 = 0
omega = 0
t0 = 0
sigma = 0
y:
E0 = 0
omega = 0
t0 = 0
sigma = 0
z:
E0 = 0
omega = 0
t0 = 0
sigma = 0
density-guided-simulation:
active = false
group = protein
similarity-measure = inner-product
atom-spreading-weight = unity
force-constant = 1e+09
gaussian-transform-spreading-width = 0.2
gaussian-transform-spreading-range-in-multiples-of-width = 4
reference-density-filename = reference.mrc
nst = 1
normalize-densities = true
adaptive-force-scaling = false
adaptive-force-scaling-time-constant = 4
grpopts:
nrdf: 43995
ref-t: 0
tau-t: 0
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Initializing Domain Decomposition on 24 ranks
NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator ‘steep’.
Dynamic load balancing: auto
Using update groups, nr 7818, average size 2.8 atoms, max. radius 0.084 nm
Minimum cell size due to atom displacement: 0.000 nm
Initial maximum distances in bonded interactions:
two-body bonded interactions: 2.580 nm, Exclusion, atoms 907 910
multi-body bonded interactions: 2.580 nm, Angle, atoms 907 910
Minimum cell size due to bonded interactions: 2.838 nm
Guess for relative PME load: 0.26
Will use 18 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 6 separate PME ranks, as guessed by mdrun
Optimizing the DD grid for 18 cells with a minimum initial size of 2.838 nm
The maximum allowed number of cells is: X 1 Y 2 Z 2
Program: gmx mdrun, version 2020-rc1-MODIFIED
Source file: src\gromacs\domdec\domdec.cpp (line 2275)
MPI rank: 0 (out of 24)
Fatal error:
There is no domain decomposition for 18 ranks that is compatible with the
given box and a minimum cell size of 2.83813 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Your problem this time is that you’re using too many CPUs given how small your box is. Gromacs is trying to divide your box into 18 (2x3x3) sub-boxes with a minimal size of 2.83 nm. If your middle box dimension is less than 3x2.83 nm, this will fail.
The easiest way to solve it is to limit the number of CPUs involved when launching gmx mdrun, with -ntmpi and -ntomp (or similar settings, depending on your compilation; check the help to mdrun with -h).
Thanks