Neha S Gandhi

13 Questions 3 Answers 0 Followers

Questions related from Neha S Gandhi

How to consider explicit water molecules in Autodock Vina docking?

I want to retain crystallographic waters in protein structure while docking a ligand. How to prepare pdbqt file in Vina considering explicit waters? Also is there any modification required in the...

05 March 2023 2,173 2 View

DPD simulation: Where can one find scripts to convert atomistic or Martini CG to DPD system for biomolecules?

Is there a way-tools (Scripts) or servers that can facilitate conversion of lipid bilayers or proteins to DPD systems? How to convert coordinate and parameter/topology file to DPD?

03 January 2022 9,110 2 View

How to map pdb file on a cryo-EM map using Chimera or other software?

The cryo-EM structure of the spike trimer (PDB 6ZB5) is in closed conformation. I have downloaded pdb file and map (EMD_11145) files for the locked conformation. I have aligned the map of the...

13 February 2021 6,143 0 View

Could anyone point to molecular mechanics force fields for selenium nanoparticles?

Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using...

25 December 2018 6,510 3 View

How to deal with water bubbles during NVT runs with position restraints in a molecular dynamics simulations??

I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...

01 March 2017 8,081 2 View

What is the role of OH group in hydroxyapaite in protein adsorption?

I have come across papers where protein adsorption is studied using molecular dynamics simulations on HAP 001 face. I would like to know if OH of HAP is involved in interactions with protein...

25 August 2016 8,642 2 View

How can we calculate CH-pi interactions from a MD trajectory?

The weak CH-pi hydrogen bond has currently been highlighted in biomolecules. I am interested in monitoring/calculating CH-pi interactions (if present between sidechains of aromatic residue and...

27 July 2016 8,932 3 View

How to calculate percentage and cumulative variance from PCA analyses in gromacs?

I have performed PCA analyses using gmx covar and anaeig tools in GROMACS. I want to calculate the percentage and cumulative percentage of the motion explained for the eigenvectors and obtain a...

27 July 2016 2,958 4 View

Is there a way to calculate boltzmann-weighted ensemble average from REMD simulation?

I have performed REMD simulation of a 25 residue long peptide. In advanced sampling techniques such REMD it is not recommended to plot parameters against time e.g. secondary structure along time...

20 October 2015 8,950 3 View

How do I calculate adsorption energy from molecular dynamics simulations?

Is there a way/equation to calculate the adsorption energy of protein at an interface from classical molecular dynamics simulation?

01 September 2015 5,786 6 View

How do I measure orientation angle between protein, and non-polar organic solvent interface?

I have a system where the protein is embedded in water box and has a non-polar interface consisting of non-polar organic molecules such as DCE. We are trying to study adsorption of protein at the...

01 September 2015 2,002 2 View

How do I calculate population size/cluster from free energy/heat maps?

I have 3 column data i.e. Phi, Psi (as bins) and free energy of the residue. I plotted this as a heatmap where the scale is from minimum 0 kcal/mol to maximum 8 kcal/mol. I want to calculate the...

16 July 2015 4,312 2 View

Is there a way to do secondary structure analyses of non standard amino acids?

I have a polymer with a single amino acid sidechain and some linear linker groups. CD studies indicate presence of peptide like beta structures. The structure is very compact in solution as seen...

16 March 2015 1,407 6 View