So is there a way we can make His neutral before running the simulations as in case of NAMD? Rabab Toubar
--- On Wed, 6/16/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: [gmx-users] Re: His protonation > To: "sagar barage" <sagarbar...@gmail.com>, "Gromacs Users' List" > <gmx-users@gromacs.org> > Date: Wednesday, June 16, 2010, 11:59 PM > > Please keep all Gromacs-related correspondence on the > gmx-users list. I am not a private tutor. > > sagar barage wrote: > > Dear sir, > > > when i was done the MD of crystal > structure the both nitrogen of immadazol ring of histidine > is protonated > > which are not protonated in crystal structure. > > There are no protons in crystal structures. > > > all histidine in > structure contain single protonation but some Histidine is > double protonated at both nitrogen > > why this happens in gromacs? > > > > Please read the manual information (or pdb2gmx -h) about > how pdb2gmx attempts to add hydrogens to the input > structure. > > -Justingm > > > -- Sagar H. Barage > > sagarbar...@gmail.com > <mailto:sagarbar...@gmail.com> > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use > the www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php