Fw: [gmx-users] AMINOACIDS
Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Thank you Fatemeh Ramezani - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 15 July 2013, 17:00 Subject: Re: [gmx-users] AMINOACIDS On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: Fw: [gmx-users] AMINOACIDS
On 7/15/13 8:54 AM, fatemeh ramezani wrote: Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Please consult any basic biochemistry text and/or website describing the Henderson-Hasselbalch equation. -Justin Thank you Fatemeh Ramezani - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 15 July 2013, 17:00 Subject: Re: [gmx-users] AMINOACIDS On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: Fw: [gmx-users] AMINOACIDS
On 7/15/13 9:11 AM, fatemeh ramezani wrote: Dear Justin I know the Henderson-Hasselbalch equation, but what should I consider [A-]/[HA] for amino acids? That's what you're solving for. You know pH and pKa, and that tells you the ratio of deprotonated to protonated species, which tells you which one predominates and therefore how you should treat them in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
