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

From: Dean Cuebas <>
Date: Fri, 16 Apr 2010 11:53:34 -0500

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

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!


> 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
> --
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> Carlos L. Simmerling, Ph.D.
> Professor, Department of Chemistry
> CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
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Received on Fri Apr 16 2010 - 10:00:07 PDT
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