AMBER Archive (2009)

Subject: [AMBER] the different RMSD?

From: qiaoyan (qiaoyan_at_dicp.ac.cn)
Date: Tue Nov 17 2009 - 20:47:42 CST

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.
2009-11-18

qiaoyan
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