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===============================================================================
11/11/16 Tinker calulations that need to be performed
===============================================================================
Analyze seems to be the main tool to gather alot of the information including:
Parameter definitions that are used
Geometric values (Bond Distances,Angles,Torsions)
Energies
>> analyze test2.xyz -k test2.q2mm.key P all
------------------------------------------------------------------------------
Interactions and Sites :
Bond Stretches 4
Angle Bends 6
Van der Waals Sites 5
Atom Type Definition Parameters :
Atom Symbol Type Class Atomic Mass Valence Description
1 C 165 165 6 12.000 4 Methane-C Param OPT
2 H 166 166 1 1.008 1 Methane-H Param OPT
3 H 166 166 1 1.008 1 Methane-H Param OPT
4 H 166 166 1 1.008 1 Methane-H Param OPT
5 H 166 166 1 1.008 1 Methane-H Param OPT
Van der Waals Parameters :
Atom Number Size Epsilon Size 1-4 Eps 1-4 Reduction
1 1 2.0400 0.0270
2 2 1.6200 0.0200 0.9230
3 3 1.6200 0.0200 0.9230
4 4 1.6200 0.0200 0.9230
5 5 1.6200 0.0200 0.9230
Bond Stretching Parameters :
Atom Numbers KS Bond
1 1 2 4.740 1.1120
2 1 3 4.740 1.1120
3 1 4 4.740 1.1120
4 1 5 4.740 1.1120
Angle Bending Parameters :
Atom Numbers KB Angle Fold Type
1 2 1 3 0.550 109.470
2 2 1 4 0.550 109.470
3 2 1 5 0.550 109.470
4 3 1 4 0.550 109.470
5 3 1 5 0.550 109.470
6 4 1 5 0.550 109.470
-------------------------------------------------------------------------------
>> analyze test2.xyz -k test2.q2mm.key D
------------------------------------------------------------------------------
Individual Bond Stretching Interactions :
Type Atom Names Ideal Actual Energy
Bond 1-C 2-H 1.1120 1.1189 0.0160
Bond 1-C 3-H 1.1120 1.5259 34.7286
Bond 1-C 4-H 1.1120 1.5261 34.7520
Bond 1-C 5-H 1.1120 1.5260 34.7403
Individual Angle Bending Interactions :
Type Atom Names Ideal Actual Energy
Angle 2-H 1-C 3-H 109.4700 109.4712 0.0000
Angle 2-H 1-C 4-H 109.4700 109.4697 0.0000
Angle 2-H 1-C 5-H 109.4700 109.4728 0.0000
Angle 3-H 1-C 4-H 109.4700 109.4743 0.0000
Angle 3-H 1-C 5-H 109.4700 109.4728 0.0000
Angle 4-H 1-C 5-H 109.4700 109.4666 0.0000
Total Potential Energy : 104.2369 Kcal/mole
Energy Component Breakdown : Kcal/mole Interactions
Bond Stretching 104.2369 4
Angle Bending 0.0000 6
------------------------------------------------------------------------------
>> analyze test2.xyz -k test2.q2mm.key M
------------------------------------------------------------------------------
Total Electric Charge : 0.00000 Electrons
Dipole Moment Magnitude : 0.000 Debyes
Dipole X,Y,Z-Components : 0.000 0.000 0.000
Quadrupole Moment Tensor : 0.000 0.000 0.000
(Buckinghams) 0.000 0.000 0.000
0.000 0.000 0.000
Principal Axes Quadrupole : 0.000 0.000 0.000
Dielectric Constant : 1.500
Effective Total Charge : 0.00000 Electrons
Effective Dipole Moment : 0.000 Debyes
Radius of Gyration : 1.281 Angstroms
Moments of Inertia and Principal Axes :
Moments (amu Ang^2) X-, Y- and Z-Components of Axes
5.163 0.707031 -0.707182 -0.000013
5.164 -0.408339 -0.408267 0.816442
6.259 -0.577378 -0.577245 -0.577427
Internal Virial Tensor : 310.496 -101.223 -101.281
-101.223 310.529 -101.151
-101.281 -101.151 310.464
-------------------------------------------------------------------------------
The tinker equivalent of the macromodel *mmo file shoule be given as:
>> analyze test2.xyz -k test2.q2mm.key M,D,P All
As for vibrational analysis, the vibrate command is used, and perhaps vibrot
can be used for torsional normal modes. This also outputs several test2.XXX
files that correspond to the individual normal mode motions.
>> vibrate test2.xyz -k test2.q2mm.key All
------------------------------------------------------------------------------
HESSIAN -- 105 Elements 100.00 % Off-diag H 0.01 % Storage
Eigenvalues of the Hessian Matrix :
1 0.000 2 0.000 3 0.000 4 71.132 5 71.142
6 132.602 7 225.599 8 225.618 9 346.870 10 346.905
11 347.696 12 959.718 13 2297.793 14 3060.139 15 3061.133
Vibrational Frequencies (cm-1) :
1 0.000 2 0.000 3 0.001 4 897.655 5 897.716
6 1245.491 7 1573.908 8 1573.973 9 1663.464 10 1663.639
11 1672.161 12 2866.074 13 3778.983 14 3928.337 15 3929.162
Vibrational Normal Mode 1 with Frequency 0.000 cm-1
Atom Delta X Delta Y Delta Z
1 0.399283 0.068477 0.189431
2 0.399283 0.068477 0.189431
3 0.399283 0.068477 0.189431
4 0.399283 0.068477 0.189431
5 0.399283 0.068477 0.189431
Vibrational Normal Mode 2 with Frequency 0.000 cm-1
Atom Delta X Delta Y Delta Z
1 0.010405 0.413004 -0.171229
2 0.010405 0.413004 -0.171229
3 0.010405 0.413004 -0.171229
4 0.010405 0.413004 -0.171229
5 0.010405 0.413004 -0.171229
Vibrational Normal Mode 3 with Frequency 0.001 cm-1
Atom Delta X Delta Y Delta Z
1 0.232722 0.338370 0.177048
2 0.232722 0.338370 0.177048
3 0.232722 0.338370 0.177048
4 0.232722 0.338370 0.177048
5 0.232722 0.338370 0.177048
Vibrational Normal Mode 4 with Frequency 897.655 cm-1
Atom Delta X Delta Y Delta Z
1 0.000579 0.023250 -0.023839
2 -0.014681 -0.587192 0.601859
3 0.176378 0.310975 0.085208
4 0.007755 0.091119 -0.084611
5 -0.176348 -0.091685 -0.318661
Vibrational Normal Mode 5 with Frequency 897.716 cm-1
Atom Delta X Delta Y Delta Z
1 -0.027196 0.014092 0.013090
2 0.686539 -0.355947 -0.330602
3 0.004080 0.188510 0.154487
4 -0.363417 -0.150954 -0.154741
5 -0.003441 0.150635 0.175023
Vibrational Normal Mode 6 with Frequency 1245.491 cm-1
Atom Delta X Delta Y Delta Z
1 0.000012 0.000013 -0.000025
2 -0.000054 -0.000030 0.000083
3 -0.408406 0.000003 0.408379
4 0.000034 0.408086 -0.408122
5 0.408280 -0.408217 -0.000038
Vibrational Normal Mode 7 with Frequency 1573.908 cm-1
Atom Delta X Delta Y Delta Z
1 -0.002882 -0.059835 0.062631
2 0.016242 0.344450 -0.360818
3 0.362565 0.405792 0.188913
4 0.019398 0.175430 -0.149139
5 -0.363895 -0.213346 -0.424559
Vibrational Normal Mode 8 with Frequency 1573.973 cm-1
Atom Delta X Delta Y Delta Z
1 -0.070704 0.037889 0.032996
2 0.407157 -0.217642 -0.189239
3 -0.036640 -0.256736 -0.312194
4 0.478709 0.319260 0.331952
5 -0.007516 -0.295948 -0.223330
Vibrational Normal Mode 9 with Frequency 1663.464 cm-1
Atom Delta X Delta Y Delta Z
1 -0.049164 0.006189 0.042560
2 -0.069255 0.008790 0.059812
3 0.536898 0.035217 -0.517674
4 -0.262581 0.139004 -0.279230
5 0.380220 -0.256695 0.230424
Vibrational Normal Mode 10 with Frequency 1663.639 cm-1
Atom Delta X Delta Y Delta Z
1 -0.021296 0.052727 -0.032323
2 -0.029925 0.073685 -0.045167
3 0.013532 0.286346 0.139850
4 -0.110524 -0.517753 0.459408
5 0.380445 -0.469982 -0.169296
Vibrational Normal Mode 11 with Frequency 1672.161 cm-1
Atom Delta X Delta Y Delta Z
1 0.065820 0.066185 0.065910
2 0.104014 0.105341 0.104592
3 -0.200333 -0.484424 -0.201928
4 -0.487987 -0.204311 -0.200646
5 -0.199266 -0.204526 -0.486665
Vibrational Normal Mode 12 with Frequency 2866.074 cm-1
Atom Delta X Delta Y Delta Z
1 0.048899 0.048904 0.048903
2 -0.570163 -0.570165 -0.570169
3 0.027127 -0.066222 0.027126
4 -0.066198 0.027082 0.027080
5 0.027107 0.027108 -0.066212
Vibrational Normal Mode 13 with Frequency 3778.983 cm-1
Atom Delta X Delta Y Delta Z
1 -0.032651 -0.032119 -0.032389
2 0.036517 0.036456 0.036487
3 0.337894 -0.325167 0.337843
4 -0.322057 0.334796 0.334815
5 0.336348 0.336279 -0.323562
Vibrational Normal Mode 14 with Frequency 3928.337 cm-1
Atom Delta X Delta Y Delta Z
1 -0.020236 0.078665 -0.058154
2 0.002026 -0.008260 0.005970
3 0.444591 -0.456203 0.451380
4 0.119197 -0.129364 -0.104845
5 -0.324912 -0.342660 0.339805
Vibrational Normal Mode 15 with Frequency 3929.162 cm-1
Atom Delta X Delta Y Delta Z
1 0.078899 -0.021982 -0.057185
2 -0.008125 0.002362 0.006021
3 -0.136303 0.126438 -0.111951
4 -0.460530 0.449181 0.455436
5 -0.334314 -0.316292 0.331264
TINKER is Exiting following Normal Termination of the Program
------------------------------------------------------------------------------
===============================================================================
11/16/16 Planning the code route
===============================================================================
While macromodel has a comment column to provide the OPT keyword when grabbing
data, I think the best way to handle this in tinker is to have another file
that has all of those parameters there. When the code is grabbing data, it
will only pick up data that is matched in the parameters file that matches
the atom types in the bond, angle, torsion.
===============================================================================
12/07/16
==============================================================================
3 terminals open
1: Testing tinker "python ../q2mm/calculate.py -tb test2.xyz" in tinker_test
2: Filetypes.py in tinker_test
3: filetypes.py on local machine
===============================================================================
12/08/16
==============================================================================
I can now calculate sp data for tinker structures. Looking at how macromodel is
setup in the code, one calculation is ran for each file. So for a freq calc
and also a minimization and also a sp, the command file is set up to run a freq
calculation, then ELST, followed by minimization and another ELST of that
structure. Therefore we will probably have to do the same thing with tinker.
Ideally it would be great if I could figure out if tinker allows for a written
output file, otherwise we will have to us shell=True for the subprocess command
inorder to write to a file (command > logfile) and append to a file (command >>
logfile)
Also in ~/q2mm/ there is a script tinker.py that has various code to pull info
from the xyz file
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