On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Hi, > > I've used the H++ server myself at times. My experience is that it's rather > sensitive to the very fine detail of the input structure in some cases. I've > had situations where H++ suggest one protonation state, then a short md > simulation takes the system to a slightly different conformation that seem > more prevalent but that yields another protonation state if sent to H++ > again. Use all biochemical knowledge that you can muster to check that the > output makes sense. Focus on residues that you suspect might be important for > the overall question you address. > > That said, pKa calculations are inherently difficult and can probably not be > done reliably without lots of simulations. As such H++ probably come close to > what we can currently accomplish within reasonable time for (nearly) static > structures. > > Best, > > Erik
Thanks for this! Is it not better just to use pK values from the literature corresponding to given residue side chain? My protein is an alpha-helix. Thanks, Steven > > 7 nov 2012 kl. 10.19 skrev Steven Neumann: > >> 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? >> >> 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? >> >> thank you, >> >> Steven >> -- >> 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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
