Re: [AMBER] To account for the protonation states of amino acids at a constant pH

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 17 Feb 2012 07:56:08 -0500

In that case, I guess you could say that leap assumes pH 7 since the standard residue names correspond to the protonation states you would expect to find at that pH.

However, to run actual constant pH simulations you should read the section on constant pH MD in the Amber manual.

(This is really nothing different than what Aron said).

All the best,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 16, 2012, at 12:22 AM, Aron Broom <broomsday.gmail.com> wrote:
> I may be off base here, but it doesn't seem like you are actually asking
> about AMBER's constant pH simulations, but just making an input file from a
> pdb.
> 
> If that is the case, then to my understanding LeAP will simply look at what
> your residue is called in the PDB.  If it is called GLU it will be the
> negatively charged, non-protonated Glutamic acid.  If it is called GLH it
> will take it to be the protonated neutral form.  So in that sense it does
> not care about pH, it just takes what you give it in your PDB.
> 
> I can't seem to read your initial message though, so perhaps you are
> actually talking about some kind of pH pKa prediction thing that LeAP can
> perform.
> 
> 
> 
> On Thu, Feb 16, 2012 at 12:01 AM, <abinayar.imsc.res.in> wrote:
> 
>> 
>> 
>> Dear Mr.David Case,
>> 
>>               Thank you very much for that. But,then H++ server takes pH
>> as an input parameter, what is the default value of pH
>> that xleap would assume?
>> 
>> Thanks in advance!
>> 
>> With regards,
>> Abinaya
>> 
>> 
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>> 
> 
> 
> 
> -- 
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Fri Feb 17 2012 - 05:00:03 PST
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