NEB QM/MM calculation. Topology error

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there is two possible reasons,one is your topology file is error another you input is error leading to error read topology file
Hi,
  I'm having some trouble running a QM/MM optimization on a system of a large protein.
I just simplify it into a smaller system that ATP interacted with the surrounding of the residues.I define the ATP segment as qm region and the rest as mm region.
  First,I take a task of prepare

Here is the input file,pre.nw:
start reac Media:Example.ogg

permanent_dir ./perm
scratch_dir ./data

charge -2

prepare
source atp.pdb
new_top new_seq
new_rst
center
orient
modify segment 952 quantum
update lists
ignore
write reac_ref.rst
write reac_ref.pdb
end

task prepare

   Then, I use the reac.top and reac_ref.rst files obtaining from the prepare task to make optimization.I possibility set some parameters smaller so that it can quickly verify.

The input file of optimization is showing below,opt.nw:
start reac

permanent_dir ./perm
scratch_dir ./data

md
system reac_ref
end

basis
  • library "6-31G"
end

dft
xc b3lyp
end

qmmm
bqzone 20.0
region qm mm
maxiter 10 1000
ncycles 2
density espfit
xyz foo
end

task qmmm dft optimize

prepare
read reac_ref.rst
write reac_opt.pdb
end

task prepare



The errors in the output file like this:

 Memory utilization after 1st SCF pass: 
Heap Space remaining (MW): 0.00 0
Stack Space remaining (MW): 12.99 12989676

  convergence    iter        energy       DeltaE   RMS-Dens  Diis-err    time
---------------- ----- ----------------- --------- --------- --------- ------
d= 0,ls=0.0,diis 1 -2625.3970221245 -6.58D+03 1.64D+01 1.78D+01 216.4
Nuclear repulsion energy = 3949.30625746002
Bq nuclear interaction energy = 5.09231130369664
WARNING: error on integrated density = 0.11D-05
greater than required accuracy of 0.10D-05
d= 0,ls=0.5,diis 2 -2282.8510692315 3.43D+02 4.07D+00 9.39D+02 247.5
Nuclear repulsion energy = 3949.30625746002
Bq nuclear interaction energy = 5.09231130369664
.................


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