On Wed, Nov 7, 2012 at 12:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/7/12 7:10 AM, Steven Neumann wrote: >> >> On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 11/7/12 4:19 AM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> I am trying to simulate protein-ligand interactions at specific pH=5. >>>> I processed my protein.pdb into the H++. As I see from th titration >>>> curve of the entire molecule it appears that at pH=5 the total charge >>>> should be equal to 2. When I process the obtained pdb from the server >>>> to pdb2gmx using -ignh I get the total charge of -3. Can anyone >>>> explain me this? >>>> >>> >>> pdb2gmx chooses protonation states based on the assumption that you're >>> working at neutral pH. If you want some alternate protonation state for >>> certain residues, you have to choose them yourself using the various >>> options >>> that pdb2gmx provides for this purpose. >> >> >> Thank you Justin. So do not understand why this server produce pdb >> file which is redundant as you have to use -his -glu etc. flags >> anyway. According to pK - this server predicts pK for each residue and >> when my pH < pKa it is protonated, otherwise it is deprotonated, >> right? How about pH = pKa ? > > > If you're using the H++ server, it has no connection to Gromacs in any way. > Your command line uses -ignh, so any hope of guessing the protonation state > from the input is lost and thus you have to use interactive selection to > counteract that effect or otherwise hope that all the atomic nomenclature is > right so that pdb2gmx doesn't complain too much. > > If pH = pKa, then your life is tougher. In solution, 50% of the residues in > the protein molecules will be protonated, 50% deprotonated. You may have to > model both protonation states if this is the case. > > > -Justin
Thank you for this! Steven > > -- > ======================================== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
