7 nov 2012 kl. 16.21 skrev Steven Neumann: > 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 >
If such (reliable) data is available, then yes. Or it may serve as validation. Erik > >> >> 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 ----------------------------------------------- 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
