Profile for:Steven yang

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Last Modified on 4:00:00 PM PST - Mon, Nov 29th 1999

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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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