Hi, Do you mean the pKa value of the side chain in solution? Or the pKa value in ethanol, DMSO, hexane? Maybe the pKa value in a membrane, or in the interior of a protein, perhaps in a hydrophobic pocket? Or the pKa with one/two/three neighbouring acidic/basic residues? If you have literature values applying to your case, sure, go ahead and use them!
Cheers, Tsjerk On Wed, Nov 7, 2012 at 4:21 PM, Steven Neumann <[email protected]>wrote: > On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund <[email protected]> > 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 [email protected] > >> 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 [email protected]. > >> * 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 > > [email protected] > > http://www2.icm.uu.se/molbio/elflab/index.html > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
