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

Chih-Ying Lin chihying2008 at gmail.com
Mon May 25 08:37:41 CEST 2009

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

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.


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