I am performing my simulations on Amber 16 and there is a lot of confusion in the tutorials.
First, we should prepare topology files for ligand and protein separately and then combine them to make a complex. right?
Second, when we do the energy minimization step we do the minimization of the whole system but in scripts complex name or any file isn't mentioned?
Third, what is the purpose of preparing gas.prm7, and wet prm7? which is more important.
and when I searched for preparation of MD script it was so confusing with long paths. is there any tutorial or online software where we can paste our files and received the md.csh file?
if anyone knows kindly respond.
Hi Syda,
You can try MDWeb or the following:
https://mmb.irbbarcelona.org/MDWeb/
https://mmb.irbbarcelona.org/MDWeb/help.php?id=tutorial
https://mmb.irbbarcelona.org/MDWeb/help.php?id=tutorialRun
https://mmb.irbbarcelona.org/MDWeb/help.php?id=tutorialAnalysis
https://mmb.irbbarcelona.org/MDWeb/htmlib/help/MDWeb_Tutorial.pdf
https://mmb.irbbarcelona.org/MDWeb/htmlib/help/MDWeb_Manual.pdf
https://www.researchgate.net/post/Does-anybody-know-a-web-server-that-is-running-Molecular-Dynamics-MD
https://biokinet.belozersky.msu.ru/easyAmber
https://gist.github.com/kspaff/1961192
https://usdkb.sandiego.edu/s/article/HPC-How-to-run-Amber-software-on-the-HPC
http://jianliugroup.pku.edu.cn/tutorial-lscivr/tutorial-lscivr.html
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