[gmx-users] minimisation with protonated residues

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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