[gmx-users] Simulation protocol for Protein-DNA-complex

Erik Marklund erikm at xray.bmc.uu.se
Sat May 26 21:11:09 CEST 2012


Are you sure this is not a periodic visualization artefact? Did you check the distane with e.g. mindist?


25 maj 2012 kl. 16.01 skrev Matthias Ernst:

> 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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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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