[gmx-users] minimisation with protonated residues

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Sep 6 17:27:53 CEST 2012

Ah okey.
Thank you for the helpful answer.

In some cases it can also be that the phosphate is not protonated at all.
Does gromacs also recognize that a proton at this position would make no
sense and remove it from the structure?

> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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