The code below shows the lowest energy found for 6 different protomers defined
by the smiles strings below as a function of number of conformers. Even with
2000 conformers I am not getting convergence to within 1 kcal/mol for
comp109_1=2.
Is this expected? Any advice or tips appreciated
200 800 1000 2500
comp109_0=0 0.16 0.16 0.16 0.16
comp109_1=1 -25.18 -24.43 -25.08 -25.18
comp109_1=2 -16.42 -16.24 -16.21 -15.15
comp109_0=3 -24.05 -24.16 -24.09 -23.96
comp109_1=5 -38.4 -37.38 -38.28 -38.32
comp109_2=8 0.18 1.38 -0.24 0.08
Code
import sys
from rdkit import Chem
from rdkit.Chem import AllChem
confs = 2500
e_cut = 20.0
decimals_in_energies = 2
filename = sys.argv[1]
file = open(filename, "r")
for line in file:
words = line.split()
name = words[0]
smiles = words[1]
m = Chem.AddHs(Chem.MolFromSmiles(smiles))
AllChem.EmbedMultipleConfs(m,numConfs=confs)
AllChem.MMFFOptimizeMoleculeConfs(m,numThreads=8,maxIters=1000,mmffVariant="MMFF94")
energies = []
for conf in m.GetConformers():
tm = Chem.Mol(m,False,conf.GetId())
prop = AllChem.MMFFGetMoleculeProperties(tm, mmffVariant="MMFF94")
ff =AllChem.MMFFGetMoleculeForceField(tm,prop)
energies.append(round(ff.CalcEnergy(),decimals_in_energies))
e_min = min(energies)
print e_min
Smiles file
comp109_0=0 C[C@@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)C[C@H](C(F)(F)F)OC(N)=N1
comp109_1=1 C[C@@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)C[C@H](C(F)(F)F)OC(=[NH2+])N1
comp109_1=2 C[C@@]1(c2cc(NC(=O)c3ccc(C#N)c[nH+]3)ccc2F)C[C@H](C(F)(F)F)OC(N)=N1
comp109_0=3 C[C@@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)C[C@H](C(F)(F)F)OC(=N)N1
comp109_1=5 C[C@@]1(c2cc(NC(=O)c3ccc(C#N)c[nH+]3)ccc2F)C[C@H](C(F)(F)F)OC(=N)N1
comp109_2=8
C[C@@]1(c2cc(NC(=O)c3ccc(C#N)c[nH+]3)ccc2F)C[C@H](C(F)(F)F)OC(=[NH2+])N1
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
