Umar Faruq Chowdhury

3 Questions 5 Answers 0 Followers

Questions related from Umar Faruq Chowdhury

How to construct complete 3D structure of a protein from two different PDB files containing two separate portions of the same protein?

Suppose, I want to model a protein's structure (containing total of 350 residues) for which there is no complete experimental structure available. However, I got two different PDB files each...

14 November 2020 9,267 3 View

Cgenff penalty score dilemma! Any solution?

I have a ligand pdbqt file (with docking co-ordinate) which I converted to mol2 file to generate a .str file. However, in the .str file, the penalty scores were more than 50 (param penalty=...

26 March 2020 5,779 1 View

How to validate ligand parameters ?

I wanted to perform a molecular dynamics simulation of a protein-ligand complex in Gromacs using the CHARMM36 force field. When generating the ligand topology file using CGenFF...

06 March 2020 2,254 6 View