Navaneet Chaturvedi

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Questions related from Navaneet Chaturvedi

Can we implement NMR restraint data in Gromacs?

Dear GMX user, We have NMR restraint data. I need to use these data in gromacs for simulation. Does Gromacs support either reading or writing NEF (NMR exchange format) format at the moment? If...

09 April 2020 9,886 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...

26 September 2016 5,647 6 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...

15 August 2016 9,311 3 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,...

17 May 2016 9,777 2 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...

17 May 2015 7,807 6 View