[gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

[Chih-Ying Lin]

Hi
I am a bit confused.
1LW9.pdb = T4 lysozyme

After this command,
pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top

=> GG 45a3    is choosed.

The Gromacs tells me that it carries +8 charges.



As we know, that the amount of charges which the protein carries is
based on pH values. So, my question is

this command =>
pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top
at what condition Gromacs calculate the charges of the protein??



Thank you
Lin








Chih-Ying Lin wrote:
> Hi
> after the command pdb2gmx,
> the protein will be added appropriate H,
>
> So, does pdb2gmx add H (protonate) based on pH =7.0 ?

No. You should choose the protonation state based on your understanding
of the conditions you wish to model, and instruct pdb2gmx accordingly.
Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there.

Mark