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

[Joshua Adelman]

Lin,

Gromacs isn't choosing a specific condition, but rather it building  
the protein using a set of defaults. Try looking at the documentation  
for pdb2gmx, which clearly states the defaults that the program uses  
for assigning the protonation state of the residues of interest.  
Given those defaults, you need to decide if they are appropriate for  
the conditions you are trying to simulate, and if not, you need to  
change them accordingly.

Josh


On May 24, 2009, at 11:37 PM, Chih-Ying Lin 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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------------------------------------------------------------------------ 
------------------------------
Joshua L. Adelman
Biophysics Graduate Group              Lab: 510.643.2159
218 Wellman Hall                                Fax: 510.642.7428
University of California, Berkeley     http://nature.berkeley.edu/ 
~jadelman
Berkeley, CA 94720 USA                   jadelman at berkeley.edu
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