AMBER Archive (2007)

Subject: Re: AMBER: calculate RMSD of only chain C

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Mar 03 2007 - 08:51:34 CST

it means #1.

On 3/2/07, 赵亚雪 <xue424_at_yahoo.com.cn> wrote:
>
> hello,
> I do molecular dynamics simulation with amber9. My system contains three
> chains - A,B and C. Now I want to calculate the RMSD of only chain C, and
> set the parameters as follows:
>
> rms reference out md1-13C_rmsd :306-387_at_CA,C,N
>
> But what really does the setting mean: (I suppose three)
> 1. Fit the chain C of trajectory to the chain C of reference and calculate
> the RMSD of only chain C
> 2. Fit the chain C of trajectory to the chain C of reference and calculate
> the RMSD of three chains
> 3. Fit the three chains of trajectory to the three chains of reference and
> calculate the RMSD of only chain C
>
> Which one is right of the three possibility (1. 2. 3.)? What I want to get
> is the first one. If it does not mean the first, how can I set the parameter
> to get it?
>
> Thanks very much!
> Yaxue Zhao
> Lab of molecular Modeing and Design
> School of Pharmacy
> East China University of Science and Technology
> Mailbox 268
> 130 Mei Long Road
> Shanghai 200237,China
> Tel: +86-21-64251190
> E-mail:xue424_at_yahoo.com.cn
>
> ------------------------------
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>
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