Arunima Verma

11 Questions 16 Answers 0 Followers

Questions related from Arunima Verma

Can someone suggest how to calculate the base-pair energy in DNA using computational tools over MD trajectory ?

I want to understand the stability of base pairs during simulations regarding energetic components.

26 March 2025 2,603 3 View

There is mismatch in the pdbs of ligand while preparing system for MD simulation in CHARMM-GUI. Can somone help me out in this ?

Here, a ligand search is done to get the CGENFF force field for serotonin. But the atom type is mismatched.

21 May 2024 9,122 2 View

How to extract the structures from 2D projection of principal component analysis of protien - ligand system in MD simulation?

So if I want to know what the structures are for different regions in the 2D projection plot of PCA analysis, how would I proceed? Any idea?

15 February 2024 5,459 2 View

Can anyone explain or provide some source on how single point (or multiple point) mutation is performed in PyMol ?

Here how means the theory or algorithm behind performing mutation in software ? OR In silico what exactly is happening here (lets say LEU is mutated to ALA) ?

25 August 2023 5,539 4 View

In MM/PBSA calculation , should we use two differnt solute dielctric constant one (in vaccum) other one (for solvation) for any sytem?

source ------https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_energy_contributions.html

13 June 2023 2,310 1 View

In MM/PBSA calculation I am getting very high error bar even greater than the energy values ,what can be reason behind this ?

Let us say binding free energy is -80, then + 130 kJ/mol error bar. So how far is it correct?

03 June 2023 5,509 5 View

How to calculate the binding free energy for DNA with two chain protein(CHAIN A, CAIN B at different position) system?

How to take the system for MM-PBSA calculation? DNA with one protein or DNA with both proteins simultaneously? Suggestions for different suitable free energy methods are appreciated.

09 May 2023 1,928 3 View

For lipid and protein interactions , can anyone suggest some techniques ?

I tried to run the python script in a tutorial of PyLipID, but the script is not working.

05 November 2022 8,792 0 View

Can Binding free energy of protein and DNA be dropped from -45 to -17 kcal/mole after mutation in protein AA. ?

Binding free energy has been done by using MM/PBSA method. Energy Values are approximated.

04 September 2022 1,457 8 View

In MM/PBSA calculation I am getting very high van der waals interaction energy in MM part ,what can be reason behind this ?

MM/PBSA is done for protein in the membrane system. Can anyone please suggest something?

10 June 2022 2,535 1 View

Can anyone tell me, Is there any change needed in .mdp files provided in MM/PBSA tutorial(link in description) while doing for PROTEIN - DNA SYSTEM?

http://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html

24 February 2022 3,977 4 View