All Questions
6 questions
7
votes
2
answers
420
views
Restrain a protein to be helical in an MD simulation
I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay ...
- 1,416
3
votes
1
answer
89
views
Perform energy minimization of multiple models of protein-dna complexes
Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)?
I know of GROMACS or Chimera or the online servers but is ...
- 131
3
votes
1
answer
576
views
Domain decomposition error while applying bonded restraints - GROMACS
GROMACS version:version 2021.3-MODIFIED
GROMACS modification: Yes
Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
- 1,461
5
votes
1
answer
687
views
Why are ligands restrained when simulating a protein-ligand complex with MD?
Currently I'm doing an MD simulation of a protein-ligand complex using GROMACS.
In the tutorial it mentioned the process of Restraining the Ligand.
Why do we do it? Is it absolutely necessary?
- 1,674
8
votes
1
answer
717
views
Alternative to CGenFF for generating large ligand topology
I am now preparing a ligand topology following GROMACS protein-ligand tutorial.
However, I have a large ligand (446 atoms).
$ wc -l my_ligand.pdb
446 my_ligand.pdb
...
- 1,674
7
votes
0
answers
169
views
How to determine minimum reasonable MD timing for ligand-protein complex [closed]
I am working on protein-ligand complex MD simulation using GROMACS.
Now I'm running the tutorial.
...
- 1,674