NEB QM/MM calculation. Topology error

Click here for full thread

Just Got Here

1:59:55 AM PDT - Tue, Jun 23rd 2015
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:

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

.................