Hi Lin, Please follow the advice to do more background reading on both biochemistry and molecular dynamics if you aren't doing so already.
The charge is not related to the pH. pH is related to the concentration of H+ in the solution, but you don't have H+ (H3O+/OH-) in your solution. The charge is what you determine it to be. You specify that an asparagine is protonated or not, and specify whether a histidine is protonated at Nd, Ne, both or none. You can make whatever choice you want, although these are not equally meaningful. If you don't explicitly specify protonation states, pdb2gmx will simple take the most common one for an amino acid free in solvent at pH 7: Asp and Glu deprotonated, Lys protonated... This has nothing to do with the expected protonation state of a protein at a certain pH. Mind that the computer doesn't think for you. It makes choices for you, and that can be a serious source of error. The computer lacks insight and chemical intuition. You'll have to provide that. That's why you have to make sure you're skilled enough in terms of the theoretical background. Cheers, Tsjerk On Mon, May 25, 2009 at 8:37 AM, Chih-Ying Lin <chihying2...@gmail.com> wrote: > Hi > I am a bit confused. > 1LW9.pdb = T4 lysozyme > > After this command, > pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top > > => GG 45a3 is choosed. > > The Gromacs tells me that it carries +8 charges. > > > > As we know, that the amount of charges which the protein carries is > based on pH values. So, my question is > > this command => > pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top > at what condition Gromacs calculate the charges of the protein?? > > > > Thank you > Lin > > > > > > > > > Chih-Ying Lin wrote: >> Hi >> after the command pdb2gmx, >> the protein will be added appropriate H, >> >> So, does pdb2gmx add H (protonate) based on pH =7.0 ? > > No. You should choose the protonation state based on your understanding > of the conditions you wish to model, and instruct pdb2gmx accordingly. > Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there. > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
