6 Questions 7 Answers 0 Followers
Questions related from Ajay Pal
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 7,306 2 View
Hi Are there any reliable pH predictors from 3d structure files of small molecules / liagnds ? Thanks
01 January 2018 9,190 0 View
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 5,881 6 View
Gromacs how to calculate Torsional angles χ1 and χ2 of a residue from gromacs MD run? which specific command?
01 January 2016 5,955 1 View
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 5,670 0 View
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 1,982 4 View