Hello,

My question is related to optimization. I increased the default optimization in "model-full.py" using the following code:

# High VTFM optimization:
a.library_schedule = autosched.slow
a.max_var_iterations = 5000

Optimization does occur, however a few amino acids are changed from their L-isomeric forms to the D-isomers.

To check if this was caused by problems with the PDB file I was using, I used a file(2KDV) from the protein databank. The same thing happens to it as well.
Also if a lower amount of optimization is used, the change from L to D forms does not occur.

Thank you in advance for the help,
Abdullah Ahmed  

---

Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now.