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, [email protected] 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
