Shir Nee Ong

5 Questions 5 Answers 0 Followers

Questions related from Shir Nee Ong

Can we use YASARA to calculate the SASA of each residues after the simulation had done?

Good day, recently I saw some journal that calculated the SASA value (y-axis) against the number of residue (x-axis) in the simulation analysis by using YASARA. So far, I only know how to get SASA...

30 December 2021 2,447 2 View

How to install Caver application ?

How do we install Caver 1.0 as a standalone application on our laptop? I tried download as usual, but the system keeps telling me the executable jar file is corrupted or invalid after I extracted...

02 July 2021 2,681 3 View

Is this a degraded DNA or a DNA that is too concentrated?

Good day, I had just extracted a plasmid DNA from a 10ml of culture (pGEX construct, as I worried that the copy number would be too low, hence I decided to take 10ml for the DNA extraction). The...

29 April 2021 7,968 1 View

How to run back my YASARA simulation(without changing the parameters)?

Good day everyone, I have run an MD simulation (lipase in 30% ethanol solution) on YASARA and planned to stop it after it reaches 50ns. However, my laboratory desktop was accidentally shut down...

05 November 2020 5,134 6 View

Does my laptop (AMD Ryzen 4300G with AMD Radeon Graphics) suitable for YASARA MD simulation?

My current laptop is Lenovo Flex 5, AMD Ryzen 4300G with AMD Radeon Graphics. I have just researched that most people recommended that Nvidia series of graphic cards but my budget can't allow me...

26 October 2020 4,923 3 View