AMBER Archive (2004)

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

From: Jiten (jiten_at_postech.ac.kr)
Date: Sat Mar 06 2004 - 01:37:27 CST

Thanks for the discussion on MD at different pH. When we assign the charges
on the residues at different pH the total charge of the protein would be
changed. According the sander MD simulations, it would force plasma charge
neutrailty. In such case should we need to neutalise the systems with
counterions before the simulation - I mean using xleap.

Your advice to me would be highly appreciated, Thanks in advance.

Jiten
----- Original Message -----
From: "Bimo Ario Tejo" <bimo7_at_gmx.de>
To: <amber_at_scripps.edu>
Sent: Saturday, March 06, 2004 1:58 PM
Subject: Re: AMBER: MD at different pH !!

> Hi Tuan,
>
> The effect of distant pHs on protein is obvious...you 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.
>
> Cheers,
> Bimo
>
> >
> > >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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