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 list gmx-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
