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 ? Steven > > >> In terms of small molecules how can I get parameters at specific pH? I >> am using Charmm and parachem.org does not support pH changes. Can >> anyone advise? >> > > pKa values for most common groups should make the protonation state at a > given pH fairly straightforward, otherwise you need to calculate the pKa's > in some way and adjust the molecule's protonation accordingly. > > -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 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
