Hi,
I have a question regarding simulation of a protein-DNA-complex where
the protein encloses the DNA double helix. I did not find a tutorial for
a system of three rather big molecules like these, that's why I ask. If
there is such, I would appreciate a hint.
I want to start with a crystal structure from PDB. When I do the steps
in J. Lemkuls tutorial "Lysozyme in water", first thing would be an
energy minimization in vacuo. Unfortunately, doing this I end up with
the two strands of the DNA double helix being far away from the protein
and seperated from each other. Can this result from clashes and
therefore high energy in the system that allows the DNA strands to move
"through" the protein or how else can this happen? And how can I prevent
this?
I mean, usually the protocol is:
- minimize system in vacuo
- add solvent and ions
- minimize again
- add thermostat and barostat
- simulate
Obviously, I cannot follow this if the first step already does not work.
When I tried to skip in-vacuo-minimization and to minimize the system in
solvent, it ended up bei either reaching machine precision without the
maximum force being small enough or in the simulation, the atom were
moving to fast. Would it be a good idea to use position restraints for
the minimizations? If yes, for which part, in which order and in which
steps?
Thank you for your help,
Matthias
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