Nilanjana Mani

7 Questions 9 Answers 0 Followers

Questions related from Nilanjana Mani

How to perform docking for ligands containing metal ions or halide ions?

Hi, I conducted virtual screening for a database using AutoDock Vina and encountered an issue with molecules containing non-bonded ions (e.g., cations like K+ or anions like Cl-, F-). It appears...

02 September 2024 294 0 View

How to do energy minimization for a large set of molecules using OpenBabel?

HI All, I'm performing energy minimization for all 31,000 ligands from the CMNP Database. The file I downloaded is a single SDF containing all the structures. I'm using the OpenBabel module in...

21 August 2024 6,361 6 View

How to extract binding energy from pv.maegz file without using Schrodinger?

I have conducted virtual screening using Schrödinger on a database of 17,000 molecules. Unfortunately, I cannot use the system with the Schrödinger license at the moment. I am trying to find a way...

19 July 2024 3,193 4 View

What is the P53 status of the colorectal adenocarcinoma cell line HCT116?

I am looking for TP53 status of various carcinoma cell line from DepMap portal (https://depmap.org/portal/gene/TP53?tab=characterization&characterization=mutation), but could not get the P53...

04 January 2024 1,689 0 View

How to extract the CDS from a whole genome using Python?

I have a file containing complete genomes of few species. I need to abstract the CDS from this.

19 July 2021 9,516 3 View

Gromacs H-Bond Calculations

GROMACS version: 2024.2 GROMACS modification: No Here post your question: I have run MD simulation of a docked membrane protein ligand complex embedded in POPC bilayer through CHARMM GUI and...

01 January 1970 5,958 6 View

How many frames to use for MMPBSA analysis?

I have performed molecular dynamics simulation for 100 ns for 6 ligands. I would like to know how many frames to use for MMPBSA analysis? Should I check the RMSD plot for each of them, identifying...

01 January 1970 4,101 3 View