Heena Bhojwani

5 Questions 1 Answers 0 Followers

Questions related from Heena Bhojwani

How to select a water model and force field for a molecular dynamics study for protein? How to decide the length of simulation?

I am working on a kinase-inhibitor complex. I wanted to perform a molecular dynamics simulation for the same. While going through the literature, I came across several options for the water model...

05 July 2020 8,091 0 View

Which RMSD value from Chimera should be considered while selecting the homology models developed using different templates?

I have developed a homology model with different templates. For checking the overall deviation from template structure, RMSD calculation was performed using Match Maker option in Chimera. It gives...

30 June 2020 7,118 0 View

Can anyone help with this error on desmond?

Traceback (most recent call last): File "/home/desmond2016-4/mmshare-v3.6/python/scripts/sim_event_analysis.py", line 1399, in _pre_analyze self._analyze() File...

28 December 2017 7,431 1 View

How to create a grid in autodock vina by using the co-crystallized ligand as reference?

I have tried to do this but I am not able to use the co-crystallized ligand as reference.

05 December 2017 2,751 2 View

Abrupt spikes in the RMSD plots for the simulation of a complex

I am working on simulation of some compounds that were identified from a virtual screen. This is one particular example wherein I am observing the spikes in the RMSD values plot over the course of...

01 January 1970 2,193 3 View