On 6/29/15 11:04 AM, Atila Petrosian wrote:
Dear Erik Thanks for your reply, I have another question. By default, Gromacs considers physiological pH value (7), am I right? Based on experimental data, my project should do under the asidic pH (2). You mentioned to pka. Should I use henderson hasselbalch equation? pH = Pka + log ([A-]/[HA]) for acids pH = Pka + log ([B]/[BH+]) for bases For amino acid Lysine (K) with pka = 10.53 ~ 11 for side chain (for simplicity, I rounded the value), 2 = 11 + log ([B]/[BH+]) ===> [BH+] = (anti log 9) [B] Thus, when I use following command pdb2gmx -f *.pdb -lys gromacs ask me: Which LYSINE type do you want for residue 14 0. Not protonated (charge 0) (LYN) 1. Protonated (charge +1) (LYS) I select 1 (Protonated) Is my rationalization true? --------------------------------------------------------------------------------------------------- and for amino acid Aspartic acid (ASP) with pka = 3.86 ~ 4 for side chain (for simplicity, I rounded the value), 2 = 4 + log ([A-]/[HA]) ===> [HA] = (antilog 2) [A-] Thus, when I use following command pdb2gmx -f *.pdb -asp gromacs ask me: Which ASPARTIC ACID type do you want for residue 18 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASH) I select 1 (Protonated) Is my rationalization true? --------------------------------------------------------------------------------------------------- If I am wrong, please guide me.
The microenvironment of an individual residue can significantly alter the pKa away from its canonial value. In some enzymes, catalytic Lys is in a hydrophobic pocket with a pKa of approximately 4! One needs to do thorough calculations of what the pKa values should be in a given protein. There are many programs, servers, etc that do this.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
