I have two conformers of molecule in .xyz files, so i need to calculate the atomic RMSD. And two methods from RDKit 2023.03.2 (python 3.10.12) gave me a different results:
from rdkit.Chem.rdmolfiles import MolFromXYZFile
from rdkit.Chem.AllChem import GetBestRMS, AlignMol
mol1 = MolFromXYZFile('mol1.xyz')
mol2 = MolFromXYZFile('mol2.xyz')
print(GetBestRMS(mol1, mol2))
# output:
>>> 1.4724067538388081
print(AlignMol(mol1, mol2))
# output:
>>> 1.6849895064063607
Also I tried another tool and obtained same results as AlignMol.
calculate_rmsd mol1.xyz mol2.xyz
>>> 1.68498950637163
Which result is more presentable and why?
Order of atoms is same in both files. Input files:
53
mol1
C -1.2878 0.5763 2.5081
C -0.0940 0.1341 1.9360
C 1.1741 0.0622 2.6960
C 2.4687 0.3699 2.3374
C 3.5742 0.1850 3.3022
C 3.2088 -0.3028 4.6335
C 4.1333 -0.5219 5.6874
C 3.7003 -0.9868 6.9197
C 2.3568 -1.2459 7.1454
C 1.4287 -1.0423 6.1369
C 1.8659 -0.5789 4.9095
C -0.1188 -0.2426 0.5911
C -1.2905 -0.1922 -0.1478
C -2.4894 0.1923 0.4610
C -2.4687 0.5937 1.7888
O -3.6751 0.1816 -0.2061
O 0.8942 -0.4005 3.9555
O 4.7477 0.4131 3.0421
O 5.4703 -0.2990 5.5706
O 1.9479 -1.7025 8.3635
H -3.7342 -0.5414 -0.8759
H 0.7834 -0.5858 0.0965
H -1.3083 0.9226 3.5342
H 5.7190 0.0308 4.6726
H 4.4198 -1.1495 7.7154
H 0.9693 -1.8444 8.3853
H 0.3762 -1.2432 6.3074
C 3.2716 2.0790 0.6209
C 2.6150 2.5024 -0.7279
H 3.0594 2.8509 1.3592
C 5.1937 1.8062 -0.8108
C 3.4610 3.5968 -1.3656
H 1.6216 2.8999 -0.5251
C 4.9268 3.0978 -1.5712
H 4.6973 0.9805 -1.3186
H 3.0327 3.8733 -2.3278
H 5.6075 3.8633 -1.2015
O 2.6447 0.8584 1.0546
O 4.6471 1.9473 0.5163
O 2.4942 1.3966 -1.6177
H 2.0475 1.6913 -2.4495
O 3.4694 4.7317 -0.5048
H 4.0197 5.4470 -0.9094
O 5.1997 2.8790 -2.9520
H 6.1446 2.6081 -3.0614
C 6.6626 1.4789 -0.6410
H 7.0930 1.2618 -1.6264
H 6.7632 0.5731 -0.0304
O 7.4024 2.5363 -0.0454
H 8.3513 2.2694 0.0342
H -3.3856 0.9228 2.2665
O -1.2365 -0.5216 -1.4668
H -1.8719 -0.0059 -2.0191
53
mol2
C -1.0014821846 0.9626299172 2.5573785856
C 0.0496599188 0.3470275666 1.8824250702
C 1.3056173719 0.0052166453 2.5515440934
C 2.5351322319 0.0505765352 1.9720897612
C 3.7184917469 -0.3826176514 2.6867783559
C 3.5033977186 -0.7447874668 4.0680019924
C 4.5710689863 -1.1496900096 4.909962476
C 4.331012171 -1.4643148376 6.2323969408
C 3.0322050126 -1.3853039034 6.7309438348
C 1.9606405974 -0.9976519507 5.9352251045
C 2.2200803246 -0.6844866633 4.6126606673
C -0.0528746879 0.1344520608 0.507116763
C -1.1219184368 0.628333423 -0.1989442937
C -2.1750118806 1.258326425 0.4749709536
C -2.1156576788 1.3988437299 1.8542332231
O -3.2301270978 1.7355182031 -0.214346733
O 1.1556575067 -0.3281667805 3.8507217244
O 4.8279324073 -0.4347069578 2.1341908715
O 5.8133601226 -1.2251560697 4.434103765
O 2.8666906888 -1.7097569209 8.0310352514
H -3.0713245174 1.5796359161 -1.1554400192
H 0.7299831889 -0.3731461741 -0.0302850043
H -0.9388459439 1.1233243801 3.6248068287
H 5.7859501611 -0.9769864865 3.4829713595
H 5.1419673986 -1.7725754551 6.8757055943
H 1.9400722545 -1.62970029 8.2788987003
H 0.9493477107 -0.9458446957 6.3149706343
C 2.5307872509 1.7951110049 0.3561613886
C 2.3639651114 1.9388506917 -1.1814462985
H 1.6479610269 2.1607641485 0.879358051
C 4.8869466139 2.2418290229 0.3490523926
C 3.6720879214 2.3746048635 -1.8740440416
H 1.6401825681 2.7355051455 -1.3532583007
C 4.8654555682 1.7945686214 -1.1212738445
H 5.2822036245 1.4119392135 0.942689672
H 3.6552784387 1.9153847486 -2.8655390874
H 5.7929240643 2.1157036397 -1.6054301121
O 2.7255144868 0.4227796783 0.6686915653
O 3.5825033241 2.5760176524 0.833928119
O 1.8260857813 0.7731060515 -1.7765584379
H 2.5260815562 0.1043987317 -1.7561092302
O 3.7348130031 3.7633538109 -2.0506663046
H 4.3080557405 4.1705571602 -1.3821917325
O 4.7612665245 0.3796800179 -1.2361215032
H 4.7275141397 -0.0164450412 -0.3543935804
C 5.7429738789 3.4584223359 0.6600871543
H 6.7326676961 3.3376535301 0.2210362026
H 5.8537268537 3.5374523689 1.7445044248
O 5.1975857627 4.658562741 0.1413912577
H 4.3744067965 4.8217632085 0.6175036702
H -2.9382623189 1.8891314043 2.3568277443
O -1.2092892555 0.5529415687 -1.5558948255
H -0.3106612492 0.4735711915 -1.9168208442
This may help
Key Differences
Alignment: AllChem.AlignMol() actually modifies the coordinates of the target molecule to align it to the reference molecule. In contrast, AllChem.GetBestRMS() doesn't modify the molecules; it only calculates the best achievable RMSD.
Optimization: AllChem.GetBestRMS() tries to find the optimal (minimum) RMSD by evaluating multiple alignments, while AllChem.AlignMol() only performs a single alignment.
Output: AllChem.AlignMol() returns the RMSD after aligning, which may not be the minimum possible RMSD. AllChem.GetBestRMS() returns the minimum RMSD possible between the two conformers.
Because of these differences, you may find that the RMSD values differ when using these two functions. If you first align the molecules using AllChem.AlignMol() and then calculate RMSD using AllChem.GetBestRMS(), you're likely to get a more accurate measure of how similar the two structures are.