AMBER Archive (2004)

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

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Fri Mar 05 2004 - 20:43:36 CST

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...:-)

Cheers,
Bimo

> At 03:30 PM 3/5/2004 +0900, you wrote:
> Hello Amber users,
>
> I am wondering if AMBER could do MD at different pH conditions. Any
> suggestions !!
>
> ----
> You should calculate the charge of residues of protein firstly (Titra or
> WHAT IF program). Secondly, you will ran MD simulation with the charge of
> residues which has been modified at each pH condition.
>
> Good luck,
>
> 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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