I'm looking to carry out conformational searches of flexible small molecules in the gas phase that I would eventually like to put through quantum chemical calculations. I used to be able to do this kind of thing using Spartan in windows, but due to cost I am trying to use TINKER with Force Field Explorer (FFE).
The problem is that the documentation is not very helpful as it doesn't go through any example cases. There is a tutorial on how to use TINKER on the command line basis, but it is based on a Linux command line input.
When I load FFE, I am able to load molecules using unoptimized PDB or MOL files. In my test case I've downloaded the MOL file of Reserpine from Chemspider - however, I have no idea how to carry out a conformational search. I click the play button but nothing happens. Additionally, there is no documentation on how to specify what type of job to carry out, etc.. I'm just so confused.
Can someone take the time to help me get started by explaining a general use case? Ideally I'd like to be able to
1. Import a geometry file of a molecule
2. Carry out a conformer search using MMFF
3. Save the 20 lowest energy conformers for QM calculations.
You can pay attention to:
http://wild.life.nctu.edu.tw/~jsyu/compchem/g09/g09ur/k_mm.htm
Hi Patrick,
I recommend Balloon and confab module in Open Babel, which are free, for conformational analysis.
http://users.abo.fi/mivainio/balloon/index.php
http://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html
Also check the following paper that I wrote:
Article A Script for Automated 3-Dimentional Structure Generation an...
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