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
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