Navaneet Chaturvedi

9 Questions 54 Answers 0 Followers

Questions related from Navaneet Chaturvedi

How to calculate water volume between interface of 2 proteins using Gromacs?

Hi I need to calculate volume of water between 2 monomer interfaces. My protein of interest is a trimer and each monomer faces its interface to other monomer. I want volume of water or number of...

05 May 2017 5,296 0 View

How to make a movement of Ub-attached-Helix in protein component by MD approach?

Dear gmx user I am Gromacs version 4.6.7 user. I am working on a protein which has Ub (Ubiquitin) binding domain having strong affinity for Ub. On one side, protein has ubiquitin binding domain...

09 September 2016 3,761 7 View

How to calculate "12-6 Lennard-Jones (LJ) Nonbonded" parameter?

Hi all, If pKa value or binding constant of a metal ion is given so How can I calculate 12-6 Lennard-Jones (LJ) Nonbonded parameter for metal ion. I need to try this parameter for my test...

08 August 2016 4,729 4 View

How can I resist isopeptide [C- - - NZ] bond through out simulation in Gromacs?

HI I have attached Ubiquitin (Ub) C-term Gly to N-term Lys of a substrate protein via iso-peptide bond [C---NZ] (for ubiquitination) using Pymol and Coot. But when I do energy minimization,...

05 May 2016 4,619 2 View

Any advice on ligand structure alignment against ligand database?

Hi All I have crystal structure of my ligand and I need to know the similar ligand structures from ligand database. Is there any tool/server which performs ligand structural alignment for my...

09 September 2015 3,969 7 View

Regarding Protein-Zn parameter in Gromacs?

Hi 1. I have four zinc ions within one protein system. I want to use a bonded model so that they could not fly out from my protein during simulation. Is there any documentation on the parameters...

09 September 2015 621 0 View

Ligand coordinates are removed after making box [protein ligand complex Molecular dynamics issue]?

Dear Scientists I want to make system for protein ligand complex for simulation study on Gromacs 4.5.6. I follow Justin tutorial...

05 May 2015 4,813 1 View

In Gromacs, how do I fix a problem regarding "Unknown left-hand 'cutoff-scheme' in parameter file"?

Hi I am working on Gromacs 4.5.6 and system contains protein+sol+Ligand. I have to neutralize the system by adding NA and CL but when I use parameter file ions.mdp (attached), the following...

05 May 2015 9,060 7 View

How can I refine an unusual bond in the protein structure?

I have attached flexible linker to a protein but found some unusual bonds (at attachment point 3-4 extra bonds found in attaching amino acid residue) at the point of attachment, I used coot for...

04 April 2015 828 4 View