Nor Azlina Ahmad

4 Questions 9 Answers 0 Followers

Questions related from Nor Azlina Ahmad

How to combine two MD runs in Gromacs?

Hello expert, I had run my sample (DNA-small molecule) for 50ns. Unfortunately, before it complete, I have electrical problem and my run was stopped. Later, I mistakenly took the wrong md.tpr...

21 July 2022 6,772 0 View

How to generate 3D structure of DNA-labelled probe for in silico study?

Hello experts, I used ChemSketch to draw DNA with the presence of probe at the 5' terminal. Later, I convert the Sketch to .sdf and .sdf to .pdb using Discovery Studio. However, when I visualized...

20 January 2022 6,114 4 View

What is the best practice on method validation in structural modelling and MD simulation?

Hello experts, I'm a beginner in structural modelling and MD simulation of DNA. Kindly share your opinion on what should I do to ensure that my structural prediction and simulation is right? Do I...

01 October 2021 1,616 6 View

How to convert .ct file to .pdb file?

I'm currently working on ssDNA aptamers 3D structure prediction. I used mfold software for 2D structure and get .ct file. For conversion, I used OpenBabel to convert it but unsuccessful. I'm not...

17 October 2018 1,036 5 View