Hello,
I am trying to optimize a transition structure for reductive elimination of two aryl groups from a palladium complex. First, I perform a constrained geometry optimization, followed by a saddle point search. The starting geometry is a guess at the transition structure obtained from a semi-empirical calculation (PM6).
When I attempt the calculation, I get the following error:
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0:geom_input: geom_verify_coords failed:Received an Error in Communication
atoms 28 and 21 are similar
atom 28 coordinates 5.9859126031747820 1.5520618613878336 2.1248825115232730
atom 21 coordinates 5.9986816421546800 1.5624167710380683 2.1126369777070719
atoms 32 and 31 are similar
atom 32 coordinates 4.3610202443823516 2.1398804915172547 2.1157016500659456
atom 31 coordinates 4.8300902223329611 2.2651109609123554 1.8443471186123299
minimum distance 2.04994050835238147E-002
************ WARNING ******************
at least two atoms are only 0.011 angstrom apart
Please check your geometry input
************ WARNING ******************
If you like danger & want to skip this check
add the following input line
set geom:dont_verify .true.
------------------------------------------------------------------------
geom_input: geom_verify_coords failed 911
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
128: end
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------
For more information see the NWChem manual at http://nwchemgit.github.io/index.php/NWChem_Documentation
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I am not certain why this error is occurring, as none of the adjusted coordinates in the output have those coordinates.
Here is my input file:
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title "OMeTrans_R_RL - constrained geometry optimization + saddle search"
- OMeTrans_R_RL.nw input deck
scratch_dir /state/partition1/tmp
echo
start
geometry noautoz noautosym nocenter
Pd -0.570460 0.192797 -0.294820
P 1.573544 -0.192393 -1.258246
C 2.259198 -1.954139 -1.522415
C 1.280930 -2.683182 -2.450445
H 0.267656 -2.700920 -2.042109
H 1.609802 -3.721328 -2.578451
H 1.240782 -2.231935 -3.447574
C 3.665529 -1.954040 -2.124607
H 4.384107 -1.461237 -1.464282
H 3.709341 -1.460653 -3.098708
H 3.997093 -2.990089 -2.264293
C 2.301895 -2.663376 -0.165865
H 1.322577 -2.680346 0.318075
H 3.022346 -2.192101 0.507587
H 2.617267 -3.703794 -0.314868
C 1.938819 0.597915 -2.939579
H 2.000820 -0.188605 -3.696281
C 2.983969 0.746470 -0.569064
O 3.246131 1.202169 -2.872607
C 3.685503 1.380353 -1.603116
C 3.420409 0.905667 0.754500
C 4.813086 2.157191 -1.364770
H 5.326893 2.630508 -2.193587
C 5.241670 2.299408 -0.051324
H 6.117660 2.903768 0.162749
C 4.558637 1.685559 0.993424
H 4.908006 1.804152 2.012816
C 2.728711 0.281536 1.913948
C 1.458765 -0.872180 4.139877
C 3.392964 -0.667273 2.718863
C 1.420039 0.622315 2.267456
C 0.779014 0.055327 3.367114
C 2.763882 -1.238498 3.823897
H -0.241817 0.347266 3.585156
H 3.276189 -1.972414 4.432889
H 0.972343 -1.323352 4.999365
O 4.648263 -1.001623 2.316737
O 0.703755 1.503175 1.490406
C 0.947489 2.886980 1.734197
H 0.240780 3.433398 1.109710
H 1.975395 3.156199 1.464921
H 0.769693 3.127101 2.789741
C -3.011977 -0.379982 -2.290770
C -2.321557 -0.697377 -1.105836
C -3.547061 -2.731714 -2.707165
C -2.212424 -2.106343 -0.749480
C -3.609867 -1.411429 -3.052895
C -2.831521 -3.113898 -1.556883
C -1.447420 -2.576309 0.354115
H -4.149054 -1.124142 -3.951355
H -3.189441 -5.215958 -1.858478
H -4.025404 -3.492465 -3.317186
C -1.324180 -3.911048 0.655049
H -0.957945 -1.847841 0.991403
H -0.728800 -4.213268 1.511540
C -1.962325 -4.886642 -0.138490
H -1.863524 -5.940483 0.103864
C -2.698112 -4.485847 -1.220696
C -3.375294 0.137157 1.292512
C -2.573518 0.647976 0.255190
C -4.537633 2.231728 1.637560
C -2.704852 2.075354 0.015702
C -4.361214 0.908824 1.940616
C -3.697133 2.857001 0.698718
C -1.831107 2.799742 -0.843494
H -4.978053 0.447848 2.702475
H -4.573652 4.801362 0.989145
H -5.299935 2.816580 2.143916
C -1.935100 4.155551 -1.038223
H -1.051968 2.247937 -1.359585
H -1.241834 4.654587 -1.709074
C -2.939742 4.898378 -0.385712
H -3.024579 5.968099 -0.549206
C -3.799582 4.250741 0.461034
C 5.345451 -1.993345 3.038807
H 6.304054 -2.111457 2.533552
H 4.809855 -2.950397 3.028083
H 5.519404 -1.690436 4.078479
C 0.943810 1.653482 -3.380383
H 1.261221 2.084976 -4.334374
H 0.878855 2.460339 -2.644773
H -0.049967 1.215388 -3.503360
C -3.236440 1.003968 -2.836729
H -3.854762 1.613431 -2.171663
H -3.749501 0.942760 -3.800012
H -2.311005 1.560694 -2.995422
O -3.186979 -1.150562 1.670945
C -4.200704 -1.854624 2.349401
H -4.289283 -1.541235 3.397283
H -3.898112 -2.902380 2.315861
H -5.172982 -1.739635 1.855931
end
basis
H library 6-31G*
C library 6-31G*
O library 6-31G*
P library def2-TZVPP
Pd library def2-TZVPP
end
dft
smear 1.0d-3
print low
print "convergence"
maxiter 600
xc m06
end
scf; thresh 1e-6; end
driver
maxiter 200
print low
end
geometry adjust # move to guess geometry & apply constraints
zcoord
bond 22 32 2.022 r constant
end
end
task dft optimize # relax with constraints
geometry adjust # release constraints
zcoord
bond 22 32 2.022 r
end
end
task dft saddle
end
task dft frequencies
vib
reuse
temp 2 398.15 498.15
end
task dft frequencies
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Any help with this is much appreciated.
Thank you.
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