Re: how to set pH

From: felmerino_at_uchile.cl
Date: Wed Mar 31 2010 - 15:01:01 CDT

Other possibility is the H++ server http://biophysics.cs.vt.edu/H++/.

Remember that these calculations have a moderately high error in the pKa of
groups. In general you should be able to do a good prediction of the protonation
state of residues that have a pKa far from the pH your are trying to simulate.
However, you need to take special care of those whose pKa is close to the pH you
want (usually histidines). If you think some of these residues es key for your
protein then you should look for some stronger method

best

felipe

> Hello,
>
> One possibility is PROPKA http://propka.ki.ku.dk/
>
> Best regards,
> Ajasja
>
> On Wed, Mar 31, 2010 at 13:29, Jrme Hnin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>
>> Hi,
>>
>> To describe pH in your system, you should look at titratable residues
>> in the protein, and decide in which protonation states these are most
>> likely to be. There are various tools to do this, depending on how
>> critical it is for you to get this right. I recommend doing some
>> bibliographic research on pKa prediction for titratable residues in
>> proteins, prediction of protonation states, etc.
>>
>> Best,
>> Jerome
>>
>>
>>
>> 2010/3/31 crazylyf <crazylyf_at_163.com>:
>> > Hi ,
>> >
>> > I am a freshman in this field and I have a question recently. I want to
>> run
>> > a simulation that has a certain pH outside of a membrane protein. Is
>> there
>> > any way can I achieve this?
>> >
>> > Thank you very much.
>> >
>> > Regards,
>> > Crick
>>
>>
>
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