Re: [AMBER] how is pH treated in Amber - other than constant pH simulations

From: Dean Cuebas <>
Date: Fri, 16 Apr 2010 15:05:43 -0500

> From: Andrew Voronkov <>
> Reply-To: AMBER Mailing List <>
> Date: Fri, 16 Apr 2010 13:17:32 -0500
> To: AMBER Mailing List <>
> Subject: Re: Re: [AMBER] how is pH treated in Amber - other than constant pH
> simulations
> Thank you that is actually what I do. The prediction by H++ server with
> isntant protonation, just wondered if this fits to Amber pH strategy without
> constant pH. As to H-bonds from Molprbity - aren't H bonds supposed to result
> mostly from MD simulations?

I might have been a bit confusing here...
What I meant was that the way that molprobity (the reduce app) adds
hydrogens to especially histidine tends to be better than H++ in that it
assigns delta versus epsilon tautomers. In fact, I've only seen H++
assigning uncharged histidines as epsilon, whereas reduce will assign delta
and visually it is very clear that a strong H-bond from another residue to
the delta H of a particular HIS is clearly preferred over an epsilon without
such h-bond stabilization. On the other hand, H++ pka predictions usually
help with deciding to have protons on both delta and epsilon nitrogens.

Of course you can go the whole mile and do an iterative process where you
now do MD on your first set of protonation predictions and then resubmit to
molprobity and H++ to see if you converge on a stable set of predictions.

> Btw as I can see many parameters like Z-score significantly improve after MD
> even against X ray structures.
> Best regards,
> Andrew
> 16.04.10, 11:53, "Dean Cuebas" <>:
>> Dear Andrew,
>> I have found the best approach to protonating my proteins is to use the pKa
>> predictions of the H++ server in conjunction with the superior H-bonding
>> prediction of reduce at the Molprobity server.
>> 1) Use Molprobity to flip Asn, Gln, His residues as needed, since MOST
>> proteins from XRC need fixing in this regard.
>> 2) Save the flipped but NOT protonated pdb to use as input to the H++ server
>> for pKa predictions.
>> 3) Continue with the Molprobity server to maximize H-bonding possibilities
>> and protonate the protein.
>> 4) Using visual inspection of the molprobity output for h-bond and clashes,
>> and the pKa predictions of H++ you can come to some reasonably confident
>> expectations, especially with regards to the correct state of histidine,
>> picking the correct HID or HIE neutral annular tautomer, or the protonated
>> HIP.
>> Realize that constant pH cannot be used with explicit water MD, so if you
>> use a water box, you should do the above.
>> Hope this helps!
>> Dean
>>> From: Carlos Simmerling
>>> Reply-To: AMBER Mailing List
>>> Date: Fri, 16 Apr 2010 11:10:42 -0500
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] how is pH treated in Amber - other than constant pH
>>> simulations
>>> simulations in amber are either constant pH or constant protonation.
>>> default protonations are reasonable for the isolated amino acids, but
>>> pka shifts may occur in proteins. it is possible to calculate pkas for
>>> the initial structure, assign protonation states, and keep them. this
>>> is ok as long as there are not conformation dependent pka changes that
>>> cross your pH.
>>> On 4/16/10, Andrew Voronkov wrote:
>>>> Dear Amber users,
>>>> when I am looking for questions about pH and Amber I get mostly information
>>>> about constant pH simulations. But what pH is supposed to be by default,
>>>> without constant pH simulations? Just neutral or what it depends from?
>>>> As I understand in Amber pH is mostly set by protonation state of the
>>>> molecules, so if not going to constant pH simulation I can approximately
>>>> imitate some pH by setting corresponding protonation state distribution of
>>>> amino acids. If physiological pH is required for protein simulation what
>>>> can
>>>> be general recommendation here - instant pH or default pH treatment?
>>>> Sincerely yours,
>>>> Andrew
>>>> _______________________________________________
>>>> AMBER mailing list
>>> --
>>> ===================================================================
>>> Carlos L. Simmerling, Ph.D.
>>> Professor, Department of Chemistry
>>> CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
>>> Stony Brook University E-mail:
>>> Stony Brook, NY 11794-5115 Web:
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Received on Fri Apr 16 2010 - 13:30:02 PDT
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