Dear Guillaume,
I am afraid I can't reproduce what you describe. Please look at the
enclosed Python script, which generates a molecule from your SMILES
string, then it attempts to embed it multiple times, and for each
embedding it carries out multiple minimizations.
If you run it with:
./mmffTuning.py -e 100 -m 10
you'll see that for each run the E column is different, which reflects
the fact that the embedded coordinates are randomly generated, and hence
give rise to a different energy, while the columns which follow (minE)
all have the same value, regardless of the min # and even of the run #
(which means that the molecule only has one stable minimum,
independently of the starting coordinates).
Kind regards,
Paolo
On 05/20/15 06:28, Guillaume GODIN wrote:
Dear All,
Can you explain me why MMFF optimization do not return the same result
if you run it multiple times ?
Is there a way to tune it to be able to converge ?
My moleucle example was : C=C1CC[C@@H]2C[C@H]1C2(C)C
best regards,
*Dr. Guillaume GODIN***
Project Manager
Innovation
CORPORATERD DIVISION
DIRECTLINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
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#!/usr/bin/env python
import sys
import copy
import argparse
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
DEFAULT_SMILES = 'C=C1CC[C@@H]2C[C@H]1C2(C)C'
parser = argparse.ArgumentParser()
parser.add_argument(-e, --embed, type = int,
help = number of times mol should be embedded)
parser.add_argument(-m, --min, type = int,
help = number of times mol should be minimized)
parser.add_argument(-s, --seed, type = int,
help = random seed)
parser.add_argument(-l, --smiles, type = str,
help = SMILES string)
args = parser.parse_args()
seed = args.seed
if (not seed):
seed = -1
smiles = args.smiles
if (not smiles):
smiles = DEFAULT_SMILES
maxEmbed = args.embed
if (not maxEmbed):
maxEmbed = 1
maxMin = args.min
if (not maxMin):
maxMin = 1
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
energyStr = '{0:10s}'.format('E')
for i in range(maxMin):
energyStr += '{0:10s}'.format('minE')
sys.stdout.write(energyStr + '\n')
for nEmbed in range(maxEmbed):
mol3d = copy.copy(mol)
AllChem.EmbedMolecule(mol3d, randomSeed = seed, useRandomCoords = True)
mp = AllChem.MMFFGetMoleculeProperties(mol3d)
ff = AllChem.MMFFGetMoleculeForceField(mol3d, mp)
energy = ff.CalcEnergy()
minEnergyList = []
for nMin in range(maxMin):
molMin = copy.copy(mol3d)
ff = AllChem.MMFFGetMoleculeForceField(molMin, mp)
if (ff.Minimize()):
sys.exit('need more iterations')
minEnergyList.append(ff.CalcEnergy())
energyStr = '{0:10.3f}'.format(energy)
for minEnergy in minEnergyList:
energyStr += '{0:10.3f}'.format(minEnergy)
sys.stdout.write(energyStr + '\n')
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