<div dir="ltr">Hi,<br><br>We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion. <br>I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not.<br>
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. <br>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.<br>
<br>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.<br>
<br>swapaa ala :22.a<br>findclash :22.a log true saveFile clash_report_22ala<br>minimize nogui true<br>write #0 test_22ala<br>swapaa val :22.a<br>findclash :22.a log true saveFile clash_report_22val<br>minimize nogui true<br>
write #0 test_22val<br>swapaa ile :22.a<br>findclash :22.a log true saveFile clash_report_22ile<br>minimize nogui true<br>write #0 test_22ile<br>...<br><br>My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each.<br>
<br>Thanks,<br><br><br>Assist.Prof.Dr. Alper YILMAZ<div><div>Department of Bioengineering</div><div>Faculty of Chemical and Metallurgical Engineering</div><div>Yildiz Technical University</div><div>Esenler, Istanbul/TURKEY 34210</div>
<div>Phone: +90.212.383-4657 (office)</div><div>Fax: +90.212.383-4625</div></div>
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