I want the low energy conformations of fructose molecule. SPARTAN software gives the conformers of a molecule but that is paid. Is there any freely available software that can give the lowest energy conformations??
SInce fructose is a small and simple molecule, you can easily guess the low energy conformations of it, which means that you can just draw them in any software (molden, molekel, avogadro to name a few) and minimize separately.
For free conformational search software see e.g. Avogadro (not sure, but should have it), Tinker or VConf from VeraChem.
Dear Deepali Sharma,
You can use ArguLab program. Using this program enables you to draw any structure and minimize it by UFF (molecular mechanics), AM1 and PM3 (semi-emperical) methods or HF (Hartree Fock).
You can use the following links for free downloading ArgusLab:
http://www.arguslab.com/arguslab.com/ArgusLab.html
http://en.freedownloadmanager.org/Windows-PC/ArgusLab-FREE.html
Hoping this will be helpful,
Rafik
Professionally, it is expected that downvoting an answer should be based on scientific reasons. If the person who downvoted my answer has the courage, he should write the reasons for his downvoting.
Thanks,
Rafik
Dear Rafik Karaman,
I very well understand that and I appreciate your answer that you posted. I don't understand how ur answer has been downvoted which I saw after I read ur msg! I have never downvoted any answer and there is no reason for downvoting any of the answers I receive for my questions posted on my RG or any other posted on RG. I personally believe its not a good practice! Currently, its difficult to assess the voter on RG who has downvoted any answer! We can ignore such voters and instead help others!
But still all my apologies since ur answer has been downvoted on RG for my question!
Regards,
Deepali Sharma
If you need it for educational purposes, than Gabedit or other desktop software can do it for you. If your goal is investigation of a series of molecules then it's better to stick to Gromacs, Amber or Tinker and do simulated annealing, that is heating a molecule to some 500-800 K and subsequent cooling to 50 K. Let's say, if you repeat this procedure 100 times you will get a hundred conformations and can make some clustering to find the best ones. Certainly, it's better to do DFT optimization of obtained geometries.
I suggest Omega to generate the conformers, and Szybki for MMFF energy calculations. After, the optimization with a DFT method, with solvation, to obtain raliable
This code uses RDKit. The UFFOptimizeMolecule optimize the conformations.
import os, sys, glob
import os.path
import shutil
from rdkit import *
from rdkit import Chem
from rdkit.Chem import AllChem
from shutil import copyfile
for filename in glob.glob(os.path.join("", "*.sdf")):
try:
f = open(filename, 'r')
print(filename)
m = Chem.ForwardSDMolSupplier(f)
for mol in m:
mol2=Chem.AddHs(mol)
AllChem.EmbedMolecule(mol2)
x = AllChem.EmbedMolecule(mol2)
if(x
Is there a way to make multiple conformations of a single molecule in RDKit and then print out each of those?
Today, the easiest, fastest, and user-friendly way is using the CREST software[1]. This software is free and based on the excellent GFN-xTB by the Grimme group.
[1] - https://github.com/grimme-lab/crest
- Badges
- Science topic
- Similar topics
- Philosophy
- Philosophy Of Science
- Reasoning