pKa of amino acid residue is a constant quantity. Depending on the pH you can protonate and deprotonate amino acid according to the pKa of particular residue.
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Nov 27, 2017 at 9:39 AM, <za...@tezu.ernet.in> wrote: > Hello Everyone > > I am trying to simulate a protein at two pH (7.4 and 9.0) using > gromacs 5.1.4. The protein has no missing residues. Optimal pH range is > 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17 > positively charged residues. > > However upon predicting the pKa values using H++ server, I am getting the > same pKa values for all the charged residues (at pH 7.4 and pH 9). And the > total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it > should have different pKa values at pH 7 and 9). > > Whether I am in the right direction or doing something wrong!!! > > Can anyone kindly suggest me how to proceed further? > > Any suggestion is appreciated. > > Thank You > Zaved > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.