Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread fatemeh ramezani
 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 -

Re: Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread Justin Lemkul
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?

Re: Fw: [gmx-users] AMINOACIDS

2013-07-15 Thread Justin Lemkul
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