Hi RDKitters, I'm having an issue using the MMFF to minimise a CORINA conformation. I've written a little script which adds hydrogens to a molecule then tries to use the MMFF forcefield to minimise the conformer. The problem is that the script hangs on the minimise step.
This error only occurs when I add hydrogens to the conformation, I assume the
reason for this is because the hydrogens are all added at the origin. Is there
a way of getting round this (in RDKit, as I want to keep the AddHs function)?
I've included the script below, it will work like this however if you switch
wrong the commented lines in the first for loop then the it no longer works.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import ChemicalForceFields
from sys import argv
suppl = Chem.SDMolSupplier(argv[1])
molList = []
for mol in suppl:
#molList.append(Chem.AddHs(mol))
molList.append(mol)
del suppl
#w = Chem.SDWriter(argv[1])
w = Chem.SDWriter('test.sdf')
for mol in molList:
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
field = AllChem.MMFFGetMoleculeForceField(mol, mp)
field.Minimize()
w.write(mol)
w.close()
Thanks in advance.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected]<mailto:[email protected]> |
W www.icr.ac.uk<http://www.icr.ac.uk/> | Twitter
@ICRnews<https://twitter.com/ICRnews>
Facebook
www.facebook.com/theinstituteofcancerresearch<http://www.facebook.com/theinstituteofcancerresearch>
Making the discoveries that defeat cancer
[cid:[email protected]]
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the addressee only. If the
message is received by anyone other than the addressee, please return the
message to the sender by replying to it and then delete the message from your
computer and network.<<inline: image001.gif>>
------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
