[gmx-users] minimisation with protonated residues
jalemkul at vt.edu
Thu Sep 6 15:41:40 CEST 2012
On 9/6/12 9:38 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I want to do a minimization of the phosphate I added to my protein. I know
> that it is protonated once. But I don't know at which position.
> How can I handle this with gromacs? Can I somehow "tell" gromacs that this
> phosphate is protonated once? Or shell I just protonate it at on position
> and run the minimization, protonate it at another position and run the
> minimization again?
You have to choose a protonation site and assign it in the structure and
topology. Minimization will find its best orientation within the local
environment, which can lead to reorientation and optimization of hydrogen
bonding and/or electrostatic interactions. I would tend to suspect that
multiple runs of EM with different protonation sites (which also requires
multiple topologies, each of which specify the different bonded parameters for
the new protonation) will likely end up the same.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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