Hi,

We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion.
I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not.
I'll write a demo script (more probably python script) to substitute certain amino acids with all standard amino acids and then minimize the structure.
As far as I know, Chimera can not calculate free energy, so I will save the PDB files and then use another program to calculate the free energy.

My first question is, whether the commands below are appropriate for my purpose or not? The sample below is a snippet from an exhaustive list. I preferred to save the information regarding clashes before the minimization just to keep record.

swapaa ala :22.a
findclash :22.a log true saveFile clash_report_22ala
minimize nogui true
write #0 test_22ala
swapaa val :22.a
findclash :22.a log true saveFile clash_report_22val
minimize nogui true
write #0 test_22val
swapaa ile :22.a
findclash :22.a log true saveFile clash_report_22ile
minimize nogui true
write #0 test_22ile
...

My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each.

Thanks,


Assist.Prof.Dr. Alper YILMAZ