Constrained Optimization Problem

Previous Topic Next Topic
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Constrained Optimization Problem

Kasper Thofte
Dear everyone

I am trying to do an optimization while constraining the distance between two atoms on two separate non-connected fragments, using the open babel python bindings with MMFF94 and conjugate gradients, with and without a preliminary random rotor search. If this distance in the input structure is close (~0.1Å) to the constraint requirement, things turn out fine, but things go badly wrong when it's not close; the molecule basically blows up, and other curiosities occur, such as the CG optimization being both instantaneous and independent of changing the number of steps from 5000 to 12000.

I have attached the python script and two initial structures, one that works and one that fails.

Any help or testimonies of similar experiences would be greatly appreciated, as I am completely out of ideas at this point.

Best regards,
Kasper Thofte
University of Copenhagen

Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
OpenBabel-discuss mailing list
[hidden email] (672 bytes) Download Attachment (1012 bytes) Download Attachment (1012 bytes) Download Attachment