4
votes
Accepted
Estimate the time between different residues?
Let the centre of mass of each residue be denoted as $r_i$ and is evaluated at every frame. Let the centre of mass of the combined system be $r_c$ where c denotes combined. You can evaluate the ...
- 4,036
2
votes
Non-Covalent Interaction between drug and DNA?
Since it has been a month since OP agreed to write an answer without actually writing the answer, I will try answering this.
The easiest way is to perform something called Enhanced Sampling ...
- 4,036
2
votes
Is there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to peptide chains for use with AMBER forcefields?
you can try use pymol to do this.
use Ctrl+middle click to pick an atom,e.g.the N atom of first residue,
then >>Build>>adresidue>>Ace. same as NME.
and save the new structure.
1
vote
What is the simplest classical force field to set up?
In order to run a molecular dynamics simulation, or a molecular mechanics calculation, you will need at least the following information:
System coordinates
Force field definitions
Molecular topology ...
- 421
1
vote
Establishing AAs protonation - which software to choose?
Propka is a standard option used to establish the protonation states of residues in MD. This is a module that can be installed in python. There is thorough documentation online regarding its use. ...
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