AMBER Archive (2009)

Subject: 回复: [AMBER] the different RMSD?

From: Rilei Yu (
Date: Tue Nov 17 2009 - 23:25:17 CST

Hi, Qiao Yan,

You can just center your ensemble, then you can calculate the accurate RMSD. You know during the MD process, the molecule will also transfer moving in different time. So you have to align all these frames, before you calculate RMSD.

Good luck!

Rilei Yu

--- 09年11月18日,周三, qiaoyan <> 写道:

发件人: qiaoyan <>
主题: [AMBER] the different RMSD?
收件人: "AMBER" <>
日期: 2009年11月18日,周三,上午10:47

Dear all:
    My initial structure is m_in.pdb, my dcd file is nptm532.dcd, the rst file is nptm532.rst and my prmtop file is m_wat.prmtop, I use ptraj to calculate the rmsd, the script is as follows:
    trajin nptm532.dcd 1 1000 50
    reference m_in.pdb
    rms reference out rms.dat "1-104_at_C,CA,N" 

then I run ptraj, the last rmsd data is 4.23673, I also use "ambpdb -p m_wat.prmtop <nptm532.rst> m32.pdb" to generate the last structure m32.pdb, then I import the two structures into pymol, align m32.pdb and resi 1-104 and name c+ca+n,m_in.pdb and resi 1-104 and name c+ca+n, the calculated rmsd is 2.118. I don't know if I have described my question clearly, thank you for your attention.

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