AMBER Archive (2004)

Subject: Re: AMBER: MD at different pH !!

From: Bimo Ario Tejo (
Date: Fri Mar 05 2004 - 22:58:39 CST

Hi Tuan,

The effect of distant pHs on protein is don't have to simulate
an alkaline enzyme which works well at pH 11 (e.g. lipase from B.
licheniformis) at pH 3; it would be denatured! As an enzymologist, I'm interested to
simulate an enzyme at some pHs nearby its optimum pH. If the optimum pH of
enzyme is 11, the simulations would be run at pHs 10, 11, and 12, but not at pH 2
or 3.

What you said is right. Histidine would have different protonation state at
different distant pHs, so you can choose to use either HIS, HIP, or HID. But
as I said, personally I'm not interested to simulate my enzyme at distant
pHs; it would be simply denatured. A small range of pH is more interesting, and
TITRA results are not compatible to be used in this case.


> >Hi Tuan,
> >
> >TITRA assigns the charge of residues, NOT the atomic charges. If let say
> the
> >charges of residue X is 0.123 in pH 7 and 0.345 in pH 8, how can you
> assign
> >this charges in AMBER? I don't think you can do it, unless if you want to
> >play around with QM calculation...:-)
> Hi Bimo,
> I'm sure that you're right. But you can not calculate QM for all of
> residues (?!). In this case, you will use TITRA for distant pHs (pH3, 6,
> 9). So you can chose the charge of residues in AMBER. :)
> Regards,
> D.A.Tuan
> Laboratory of Molecular Biotechnology - Collaborative Bioinformatics Lab.
> University of Natural Sciences
> Vietnam National University - Ho Chi Minh City
> 227 Nguyen Van Cu St., Dist. 5, HCM City, Vietnam
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