AMBER Archive (2004)

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

From: Do Anh Tuan (datuan_at_hcmuns.edu.vn)
Date: Fri Mar 05 2004 - 22:20:04 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...:-)

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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