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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 25 08:49:55 CEST 2009

Hi Lin,

Please follow the advice to do more background reading on both
biochemistry and molecular dynamics if you aren't doing so already.

The charge is not related to the pH. pH is related to the
concentration of H+ in the solution, but you don't have H+ (H3O+/OH-)
in your solution. The charge is what you determine it to be. You
specify that an asparagine is protonated or not, and specify whether a
histidine is protonated at Nd, Ne, both or none. You can make whatever
choice you want, although these are not equally meaningful. If you
don't explicitly specify protonation states, pdb2gmx will simple take
the most common one for an amino acid free in solvent at pH 7: Asp and
Glu deprotonated, Lys protonated... This has nothing to do with the
expected protonation state of a protein at a certain pH.

Mind that the computer doesn't think for you. It makes choices for
you, and that can be a serious source of error. The computer lacks
insight and chemical intuition. You'll have to provide that. That's
why you have to make sure you're skilled enough in terms of the
theoretical background.



On Mon, May 25, 2009 at 8:37 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
> 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
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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