8 Questions 17 Answers 0 Followers
Questions related from Tomasz Molcan
I would like to perform MD simulation study for CYP450 proteins in gromacs 4.6.7 with gromos53a6.ff. When I prepare the system for simulation, i have got error that gb_, ga_ and gd_ were not found...
04 April 2016 9,091 3 View
I have 3 X-ray structures with co-crystallized ligand in active site. How should I actively copy all ligand in this same position from all temple to the final homology models? I perform homology...
02 February 2015 996 3 View
How should I perform correct equilibration of my protein before I run molecular dynamics.
07 July 2014 1,383 6 View
Charmm27 or Charmm36?
05 May 2014 4,859 2 View
I have done a 50 ns molecular dynamics symulatuion for protein-peptyde complex in NAMD, and now I want to calculate strenght of the protein-peptide interaction. What is the best way or ways to the...
04 April 2014 7,457 4 View
I have to predict 3D structure of protein with long (70 a.a) N-terminal disorder region. Is there any best method for predicting the fold for this disorder region, or only way is use molecular...
03 March 2014 6,051 5 View
Is there a good way to add crystallographic water to structure used, for example, dowser software, while preparing protein structures for molecular dynamics simulations?
03 March 2014 2,428 8 View
Does NAMD2 work with stream technologies for molecular dynamics calculations like CUDA cores?
02 February 2014 9,299 3 View
