...and find the lowest energy conformer

Hello:


I should have mentioned in my last post that I would also like to use action strings with the standardizer to find the lowest energy conformer, starting with a 2D molecule. Is this automatically done using clean:full? However, as I posted before, use of ..clean:full.. does not convert a 2D mol file into a 3D one.


John

3D clean tries to give the lowest energy conformer but it is not guaranteed. It gives a "local minimum" but it is not known whether it is also the global minimum or not. We have a clean option which increases the processing time but also increases the probability of finding the lowest energy conformer. Currently this option is not available in Standardizer but I will also add this in JChem 3.2.

In the latest version or JChem, what would be the steps to find the global minimum (lowest energy conformer) rather than the local minimum? The increase in processing time is not a concern.

 

Thanks,

Graham 

gwatts wrote:

In the latest version or JChem, what would be the steps to find the global minimum (lowest energy conformer) rather than the local minimum? The increase in processing time is not a concern.   Thanks, Graham

Hi Graham,

molconvert -H3D may help you. However the help lacks examples and thats why it may a bit hard to interpret. It will improve.

The

molconvert -3:[ca]{1}{50} mol test.smiles -o testCA.mol

command you need.

[ca] means conformational analysis

1 means save only the first and lowest energy conformer

50 means try to generate maximum 50 conformers.

 

Adrian,

This was exactly the command I was looking for. This is perfect. Thanks you very much for your help, I appreciate it very much.

Thanks,

Graham