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CMMDE
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Added xTB Standalone Support

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Aditya Wibawa Sakti 2 years ago
parent d4be395790
commit 58a1f9020d
33 changed files with 15361 additions and 1 deletions
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  1. 4
      README.md
  2. BIN
      README.pdf
  3. 19
      bin/cmmde.py
  4. 86
      cmmde_gui/test/naftalena/cmmd.engrad
  5. BIN
      cmmde_gui/test/naftalena/cmmd.gbw
  6. 8
      cmmde_gui/test/naftalena/cmmd.in
  7. 1844
      cmmde_gui/test/naftalena/cmmd.opt
  8. 2798
      cmmde_gui/test/naftalena/cmmd.out
  9. BIN
      cmmde_gui/test/naftalena/cmmd.xtbrestart
  10. 20
      cmmde_gui/test/naftalena/cmmd.xyz
  11. 6
      cmmde_gui/test/naftalena/cmmd_property.txt
  12. 120
      cmmde_gui/test/naftalena/cmmd_trj.xyz
  13. 1
      cmmde_gui/test/naftalena/geom.smi
  14. 20
      cmmde_gui/test/naftalena/geom.xyz
  15. 10
      cmmde_gui/test/naftalena/run.sh
  16. 8
      cmmde_gui/test/naftalena/run_babel.sh
  17. 1
      cmmde_gui/test/naftalena/slurm-2850.out
  18. 0
      cmmde_gui/test/naftalena/slurm-2851.out
  19. 0
      examples/xtb/.xtboptok
  20. 75
      examples/xtb/charges
  21. 6
      examples/xtb/cmmd.in
  22. 77
      examples/xtb/geom.xyz
  23. 8
      examples/xtb/run.sh
  24. 2
      examples/xtb/slurm-2858.out
  25. 100
      examples/xtb/wbo
  26. 1768
      examples/xtb/xtb.out
  27. 385
      examples/xtb/xtbopt.log
  28. 77
      examples/xtb/xtbopt.xyz
  29. BIN
      examples/xtb/xtbrestart
  30. 7700
      examples/xtb/xtbscan.log
  31. 160
      examples/xtb/xtbtopo.mol
  32. BIN
      lib/__pycache__/cmmde_xtb.cpython-39.pyc
  33. 59
      lib/cmmde_xtb.py

4
README.md
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@ -9,7 +9,8 @@ This software is developed for decreasing the barrier in using popular open-sour
4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm) 4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm)
5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en) 5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en)
6. [Quantum Espresso](https://www.quantum-espresso.org/) 6. [Quantum Espresso](https://www.quantum-espresso.org/)
7. [xTB via Orca](https://github.com/grimme-lab/xtb) 7. [xTB](https://github.com/grimme-lab/xtb)
8. [Open Babel](http://openbabel.org/wiki/Main_Page)
## About CMMDE ## About CMMDE
CMMDE is a set of tools based on Python for running computational jobs, as well as analyzing, visualizing, and post-processing the results in free/libre and open source applications for computational molecular & material design. CMMDE is a set of tools based on Python for running computational jobs, as well as analyzing, visualizing, and post-processing the results in free/libre and open source applications for computational molecular & material design.
@ -47,3 +48,4 @@ cd CMMDE
chmod +x install.sh chmod +x install.sh
./install.sh ./install.sh
``` ```

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19
bin/cmmde.py
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@ -9,6 +9,7 @@ from cmmde_mdpro import proprep, ligprep
from cmmde_dftb import poscar2gen, vasp2gen, dftb from cmmde_dftb import poscar2gen, vasp2gen, dftb
from cmmde_qe import qe from cmmde_qe import qe
from cmmde_nw import nwchem from cmmde_nw import nwchem
from cmmde_xtb import xtb
import time import time
@ -113,6 +114,20 @@ parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan d
parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.') parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.')
# Input untuk simulasi MD sistem protein # Input untuk simulasi MD sistem protein
parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb') parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb')
# Input untuk perkiraan jalur reaksi menggunakan xTB
parser.add_argument('-nrun','--nrun',type=int,default=1,help='Jumlah banyaknya sampling path yang dilakukan. Default: 1.')
parser.add_argument('-npoint','--npoint',type=int,default=25,help='Jumlah banyaknya titik untuk interpolasi jalur reaksi. Default: 25.')
parser.add_argument('-anopt','--anopt',type=int,default=10,help='Jumlah maksimum step optimasi geometri yang dilakukan. Default: 10.')
parser.add_argument('-kpush','--kpush',type=float,default=0.003,help='Faktor skala untuk variasi nilai RMSD. Default: 0.003 atomic unit.')
parser.add_argument('-kpull','--kpull',type=float,default=-0.015,help='Tetapan pegas untuk menarik posisi atom. Default: -0.015 atomic unit.')
parser.add_argument('-ppull','--ppull',type=float,default=0.05,help='Kekuatan tarikan pegas teroptimasi. Default: 0.05 atomic unit.')
parser.add_argument('-alp','--alp',type=float,default=1.2,help='Lebar potensial Gaussian dalam satuan Angstrom. Default: 1.2 Angstrom.')
# Scanning geometri menggunkaan xTB standalone
parser.add_argument('-dist','--distance',type=str,default='None',help='Jarak antara dua buah atom dalam format: Serial1,Serial2,Jarak. Contoh: 4,1,1.5.')
parser.add_argument('-ang','--angle',type=str,default='None',help='Sudut antara tiga buah atom dalam format: Serial1,Serial2,Serial3,Sudut. Contoh: 4,1,3,180.')
parser.add_argument('-dih','--dihedral',type=str, default='None',help='Sudut dihedral antara empat buah atom dalam format: Serial1,Serial2,Serial4,Dihedral. Contoh: 4,1,3,2,120.')
parser.add_argument('-scanmode','--scanmode',type=str,default='None',help='Mode scan geometri yang diinginkan. Pilihan: concerted, sequential.')
parser.add_argument('-scan','--scan',type=str,default='None',help='Rentang Scanning dalam format: Titik1,Titik2,JumlahTitik. Contoh:2.5,1.0,100.')
# Input untuk perhitungan NEB # Input untuk perhitungan NEB
parser.add_argument('-produk','--produk',type=str,help='Struktur produk yang digunakan dalam interpolasi NEB dalam format koordinat Cartesian.') parser.add_argument('-produk','--produk',type=str,help='Struktur produk yang digunakan dalam interpolasi NEB dalam format koordinat Cartesian.')
parser.add_argument('-trans','--transitionstate',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.') parser.add_argument('-trans','--transitionstate',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.')
@ -382,3 +397,7 @@ if opt.job == 'proprep' and opt.software == 'gmx':
proprep(opt.protein) proprep(opt.protein)
if opt.job == 'ligprep' and opt.software == 'gmx': if opt.job == 'ligprep' and opt.software == 'gmx':
ligprep(opt.ligand,opt.charge) ligprep(opt.ligand,opt.charge)
# Program XTB Standalone
if opt.software == 'xtb':
xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan)

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cmmde_gui/test/naftalena/cmmd.engrad
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@ -0,0 +1,86 @@
#
# Number of atoms
#
18
#
# The current total energy in Eh
#
-25.474385516520
#
# The current gradient in Eh/bohr
#
-0.000136215505
-0.000372377899
0.000001125693
-0.000132249935
0.000376634673
0.000002669203
0.000357078532
-0.000224212188
0.000007912916
-0.000003964442
0.000017074061
-0.000008976009
-0.000353164526
-0.000221756001
0.000006723727
0.000135880120
0.000372858276
0.000002848800
0.000131832079
-0.000373743978
0.000001854847
-0.000350246704
0.000220407573
0.000009477425
0.000002173643
-0.000012418889
-0.000013471275
0.000348731937
0.000220360870
0.000011264482
-0.000020605813
-0.000175411648
0.000006625481
-0.000021212117
0.000174448040
0.000000948031
0.000114956161
0.000060577107
-0.000013873284
-0.000115141875
0.000061148015
-0.000002672329
0.000020795481
0.000175133815
0.000005963698
0.000021199049
-0.000175385467
-0.000000735846
-0.000115264276
-0.000061390100
-0.000010707029
0.000115418193
-0.000061946260
-0.000006978532
#
# The atomic numbers and current coordinates in Bohr
#
6 4.5571258 -1.3287702 -0.0053890
6 4.5586789 1.3246830 -0.0046449
6 2.3301840 2.6290412 -0.0054059
6 -0.0043626 1.3419232 -0.0066633
6 -2.3374022 2.6317647 -0.0063895
6 -4.5674083 1.3299860 -0.0071734
6 -4.5689557 -1.3234642 -0.0086870
6 -2.3404501 -2.6278162 -0.0090882
6 -0.0059212 -1.3406585 -0.0078041
6 2.3271077 -2.6305315 -0.0071662
1 6.3357317 -2.3312669 -0.0045097
1 6.3384594 2.3250895 -0.0035117
1 2.3219079 4.6720601 -0.0051436
1 -2.3267515 4.6747709 -0.0055138
1 -6.3460252 2.3324659 -0.0065981
1 -6.3487246 -2.3238910 -0.0095580
1 -2.3321575 -4.6708323 -0.0104583
1 2.3164424 -4.6735365 -0.0081448

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cmmde_gui/test/naftalena/cmmd.in
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@ -0,0 +1,8 @@
#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
*xyzfile 0 1 geom.xyz

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cmmde_gui/test/naftalena/cmmd.opt
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cmmde_gui/test/naftalena/cmmd.out
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cmmde_gui/test/naftalena/cmmd.xyz
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@ -0,0 +1,20 @@
18
Coordinates from ORCA-job cmmd
C 2.41152713335072 -0.70315491965030 -0.00285175640619
C 2.41234899929286 0.70099206550767 -0.00245799823640
C 1.23308025141841 1.39122869364744 -0.00286066883031
C -0.00230860377905 0.71011519433099 -0.00352606339333
C -1.23689996102567 1.39266987428458 -0.00338118661967
C -2.41696837199262 0.70379830277779 -0.00379601125133
C -2.41778724238201 -0.70034709816064 -0.00459698849307
C -1.23851286123808 -1.39058044924232 -0.00480925033694
C -0.00313334505810 -0.70944594331312 -0.00412973845697
C 1.23145236016325 -1.39201734055467 -0.00379216955028
H 3.35272482327401 -1.23365329886495 -0.00238641187896
H 3.35416825449150 1.23038438861012 -0.00185831172794
H 1.22870075528791 2.47234771346020 -0.00272186442839
H -1.23126388682849 2.47378219283471 -0.00291778014193
H -3.35817188229753 1.23428779710778 -0.00349157352384
H -3.35960034895426 -1.22975017185378 -0.00505785398497
H -1.23412458879329 -2.47169798545112 -0.00553432039391
H 1.22580851507043 -2.47312901547039 -0.00431005234558

6
cmmde_gui/test/naftalena/cmmd_property.txt
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@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

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cmmde_gui/test/naftalena/cmmd_trj.xyz
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@ -0,0 +1,120 @@
18
Coordinates from ORCA-job cmmd E -25.471091538490
C 2.431150 -0.696950 -0.009500
C 2.431520 0.694960 -0.003620
C 1.222970 1.392930 0.006450
C -0.002180 0.707060 0.004490
C -1.226640 1.394340 -0.001370
C -2.436240 0.697810 -0.010170
C -2.437350 -0.694110 -0.005370
C -1.229030 -1.392640 0.003820
C -0.003150 -0.707300 0.004240
C 1.221920 -1.394170 -0.001390
H 3.371650 -1.241270 -0.021400
H 3.372300 1.239120 -0.009030
H 1.243380 2.480380 0.012260
H -1.246110 2.481860 -0.004220
H -3.376340 1.243070 -0.022020
H -3.378530 -1.237370 -0.011250
H -1.250140 -2.480170 0.007200
H 1.241860 -2.481720 -0.003600
18
Coordinates from ORCA-job cmmd E -25.473780379000
C 2.414135 -0.699086 -0.006775
C 2.414821 0.696963 -0.003313
C 1.226571 1.391929 0.001600
C -0.002248 0.710122 0.000415
C -1.230322 1.393304 -0.002910
C -2.419482 0.699799 -0.007574
C -2.420363 -0.696257 -0.005261
C -1.232213 -1.391384 -0.000676
C -0.003141 -0.709920 -0.000088
C 1.225136 -1.392847 -0.003148
H 3.349911 -1.238622 -0.012404
H 3.351074 1.235770 -0.004726
H 1.245529 2.472464 0.005901
H -1.248272 2.473872 -0.003264
H -3.355040 1.239745 -0.013198
H -3.356808 -1.234683 -0.007451
H -1.251490 -2.471930 0.001927
H 1.243243 -2.473410 -0.003535
18
Coordinates from ORCA-job cmmd E -25.474250159220
C 2.409372 -0.701688 -0.004234
C 2.410206 0.699518 -0.002826
C 1.231309 1.391746 -0.001635
C -0.002290 0.711390 -0.002322
C -1.235103 1.393136 -0.003468
C -2.414829 0.702338 -0.005136
C -2.415627 -0.698874 -0.004917
C -1.236757 -1.391091 -0.003651
C -0.003136 -0.710880 -0.002942
C 1.229694 -1.392523 -0.003833
H 3.346481 -1.238191 -0.005706
H 3.347900 1.234992 -0.002411
H 1.242874 2.471682 0.000280
H -1.245553 2.473090 -0.002787
H -3.351855 1.238953 -0.006690
H -3.353384 -1.234256 -0.005517
H -1.248416 -2.471034 -0.002835
H 1.240154 -2.472478 -0.003851
18
Coordinates from ORCA-job cmmd E -25.474340578150
C 2.410431 -0.702683 -0.003226
C 2.411276 0.700516 -0.002585
C 1.232875 1.391504 -0.002623
C -0.002301 0.711012 -0.003220
C -1.236680 1.392919 -0.003459
C -2.415892 0.703325 -0.004167
C -2.416694 -0.699877 -0.004722
C -1.238297 -1.390844 -0.004565
C -0.003135 -0.710403 -0.003846
C 1.231233 -1.392275 -0.003864
H 3.349295 -1.237016 -0.003303
H 3.350750 1.233761 -0.001892
H 1.237573 2.472109 -0.001927
H -1.240194 2.473532 -0.002746
H -3.354723 1.237695 -0.004374
H -3.356190 -1.233098 -0.005103
H -1.243024 -2.471455 -0.004763
H 1.234735 -2.472892 -0.004095
18
Coordinates from ORCA-job cmmd E -25.474383190250
C 2.411713 -0.703268 -0.002655
C 2.412543 0.701105 -0.002420
C 1.233412 1.391150 -0.003072
C -0.002309 0.710208 -0.003696
C -1.237229 1.392591 -0.003385
C -2.417159 0.703909 -0.003610
C -2.417976 -0.700463 -0.004573
C -1.238836 -1.390499 -0.004997
C -0.003134 -0.709532 -0.004306
C 1.231774 -1.391934 -0.003807
H 3.352543 -1.234568 -0.001942
H 3.353998 1.231293 -0.001736
H 1.230048 2.472315 -0.003163
H -1.232613 2.473751 -0.002858
H -3.357996 1.235197 -0.003066
H -3.359423 -1.230666 -0.004969
H -1.235459 -2.471664 -0.005897
H 1.227145 -2.473095 -0.004328
18
Coordinates from ORCA-job cmmd E -25.474385516520
C 2.411527 -0.703155 -0.002852
C 2.412349 0.700992 -0.002458
C 1.233080 1.391229 -0.002861
C -0.002309 0.710115 -0.003526
C -1.236900 1.392670 -0.003381
C -2.416968 0.703798 -0.003796
C -2.417787 -0.700347 -0.004597
C -1.238513 -1.390580 -0.004809
C -0.003133 -0.709446 -0.004130
C 1.231452 -1.392017 -0.003792
H 3.352725 -1.233653 -0.002386
H 3.354168 1.230384 -0.001858
H 1.228701 2.472348 -0.002722
H -1.231264 2.473782 -0.002918
H -3.358172 1.234288 -0.003492
H -3.359600 -1.229750 -0.005058
H -1.234125 -2.471698 -0.005534
H 1.225809 -2.473129 -0.004310

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cmmde_gui/test/naftalena/geom.smi
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c2ccc1ccccc1c2

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cmmde_gui/test/naftalena/geom.xyz
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18
C 2.43115 -0.69695 -0.00950
C 2.43152 0.69496 -0.00362
C 1.22297 1.39293 0.00645
C -0.00218 0.70706 0.00449
C -1.22664 1.39434 -0.00137
C -2.43624 0.69781 -0.01017
C -2.43735 -0.69411 -0.00537
C -1.22903 -1.39264 0.00382
C -0.00315 -0.70730 0.00424
C 1.22192 -1.39417 -0.00139
H 3.37165 -1.24127 -0.02140
H 3.37230 1.23912 -0.00903
H 1.24338 2.48038 0.01226
H -1.24611 2.48186 -0.00422
H -3.37634 1.24307 -0.02202
H -3.37853 -1.23737 -0.01125
H -1.25014 -2.48017 0.00720
H 1.24186 -2.48172 -0.00360

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cmmde_gui/test/naftalena/run.sh
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@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

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cmmde_gui/test/naftalena/run_babel.sh
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@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

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cmmde_gui/test/naftalena/slurm-2850.out
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1 molecule converted

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cmmde_gui/test/naftalena/slurm-2851.out
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examples/xtb/.xtboptok
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75
examples/xtb/charges
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@ -0,0 +1,75 @@
-0.57867945
0.12330482
0.12689908
-0.09189003
0.08606314
-0.15696977
-0.01388823
0.01115225
0.00725991
0.01061040
0.00796883
0.00977780
-0.00447685
-0.01491119
-0.02978050
-0.02722387
-0.02961502
-0.02761892
0.03078032
0.08954994
0.03647950
0.03209002
0.02999592
-0.02724929
-0.02062862
-0.02554303
-0.02640057
-0.02772187
0.03489772
0.03646840
0.03380933
0.05679178
0.03946764
-0.02790415
-0.02834971
-0.02765220
-0.02865682
-0.01768288
0.05257133
0.03096555
0.02916248
0.03055154
0.03160205
-0.02959759
-0.02898275
-0.02946099
-0.03004953
-0.02602992
0.03353371
0.02862262
0.03347012
0.02916001
0.02595951
-0.01279610
-0.02732544
-0.02718452
-0.02695659
-0.02838905
0.03344760
0.08045090
0.03603254
0.03336957
0.03126512
-0.01839450
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6
examples/xtb/cmmd.in
Unescape View File

@ -0,0 +1,6 @@
$constrain
distance: 1,2,1.4
$scan
1: 4,1.4,100
$opt
maxcycle = 500

77
examples/xtb/geom.xyz
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@ -0,0 +1,77 @@
75
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8
examples/xtb/run.sh
Unescape View File

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
$XTB_COMMAND geom.xyz --opt -P 1 --input cmmd.in > xtb.out

2
examples/xtb/slurm-2858.out
Unescape View File

@ -0,0 +1,2 @@
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
normal termination of xtb

100
examples/xtb/wbo
Unescape View File

@ -0,0 +1,100 @@
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1768
examples/xtb/xtb.out
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File diff suppressed because it is too large Load Diff

385
examples/xtb/xtbopt.log
Unescape View File

@ -0,0 +1,385 @@
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77
examples/xtb/xtbopt.xyz
Unescape View File

@ -0,0 +1,77 @@
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examples/xtb/xtbtopo.mol
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xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
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# CMMDE function for xTB standalone program
import os
def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan):
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD""".format(nproc),file=fout)
if 'opt' in job:
print("$XTB_COMMAND {} --opt -P {} > xtb.out".format(geom,nproc),file=fout)
if 'freq' in job:
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
if 'opt' in job and 'freq' in job:
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in > xtb.out".format(geom,nproc),file=fout)
if 'path' in job:
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} > xtb.out".format(geom,product,nproc),file=fout)
if 'scan' in job:
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
if 'freq' in job:
with open('cmmd.in', 'w') as f:
print("""$thermo
temp={}""".format(temperature),file=f)
if 'path' in job:
with open("cmmd.in", 'w') as f:
print("""$path
nrun={}
npoint={}
anopt={}
kpush={}
kpull={}
ppull={}
alp={}
$end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
if 'scan' in job:
with open("cmmd.in",'w') as f:
print("$constrain",file=f)
if distance != 'None':
print("distance: {}".format(distance),file=f)
if angle != 'None':
print("angle: {}".format(angle),file=f)
if dihedral != 'None':
print("dihedral: {}".format(dihedral),file=f)
print("$scan",file=f)
if scanmode != 'None':
print("mode = {}".format(scanmode),file=f)
scan = scan.split(";")
for index, i in enumerate(scan):
print("{}: {}".format(index+1,i),file=f)
print("""$opt
maxcycle = {}""".format(maxiter),file=f)
os.system('sbatch run.sh')
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