[gmx-users] pH

[Atila Petrosian]

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?
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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?
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If I am wrong, please guide me.