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. https://signup.live.com/signup.aspx?id=60969