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.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

constropt.py (672 bytes) Download Attachment
AmideRfail.xyz (1012 bytes) Download Attachment
AmideRworks.xyz (1012 bytes) Download Attachment