Ajay Pal

6 Questions 7 Answers 0 Followers

Questions related from Ajay Pal

Water bonds elongating during NPT equilibrium (GROMACS) ?

Hi I am running lipid bilayer (POPC) equilibrium simulation solvated with spc water molecules. (full membrane protein) The NVT ensemble has no water bond elongation or jumpimg from 1 leaflet...

01 January 2018 7,303 2 View

In silico pH predictor ?

Hi Are there any reliable pH predictors from 3d structure files of small molecules / liagnds ? Thanks

01 January 2018 9,186 0 View

Extract energy from .edr file for specific group if atoms

I performed MD simulations of an Ag-Ab complex. GROMACs treat the whole Ag-Ab complex as Protein in topology file. And I didn't provide index file which grouped Antigen and L-chain Ab and H-chain...

08 August 2017 5,874 6 View

How do I calculate Torsional angles χ1 and χ2 of a residue in gromacs analysis ?

Gromacs how to calculate Torsional angles χ1 and χ2 of a residue from gromacs MD run? which specific command?

01 January 2016 5,949 1 View

VMD : window name "id4" already exists in parent ?

Hi I am trying Alanine Scanning in VMD with a proteinn containing 3 chains. Chain A : 4-109 aa Chain B: 1-200 aa Chain C: 1-200 aa I created .psf (autopsf gen) and .pdb files and have an .xtc...

01 January 1970 5,667 0 View

Ligand_protein complex in Lipid Bilayer Gromacs MD simulation - diverging due to protin and liagnd constaints.

Hello I am running protein-ligand complex simulations- with protein embedded in lipid bilayer and solvated + ionized as per standard rules of Gromacs. After complete Energy minimization - in NVT...

01 January 1970 1,975 4 View