AMBER Archive (2009)

Subject: Re: Re: [AMBER] the different RMSD?

From: qiaoyan (qiaoyan_at_dicp.ac.cn)
Date: Fri Nov 13 2009 - 22:16:27 CST


dear professor:
   the script I used is as follows:
trajin nptm501.dcd 1 1000 20
trajin nptm502.dcd 1 1000 20
trajin nptm503.dcd 1 1000 20
trajin nptm504.dcd 1 1000 20
trajin nptm505.dcd 1 1000 20
trajout 10ns.dcd
reference m_in.pdb
rms reference out rms.dat ":1-104_at_C,CA,N" time 40
I select the initial structure as reference, when I check the rms.dat, it is very large,I also use the rst file to generate the pdb file, when I align this structure to the initial structure(m_in.pdb) using the same restraint:
 align m5.pdb and resi 1-104 and name c+ca+n,m_in and resi 1-104 and name c+ca+n
 the rmsd is only about 2
I don't know if I have described clearly, thank you for your attention!

2009-11-14



qiaoyan



发件人： Thomas Cheatham
发送时间： 2009-11-14 11:41:11
收件人： qiaoyan_at_dicp.ac.cn; AMBER Mailing List
抄送：
主题： Re: [AMBER] the different RMSD?
 
> I use ptraj to analyze my result, the rmsd goes up to more than
> 6,but when I load the same structure to the Pymol using the identical
> reference structure, the rmsd was only about 2, I am very confused about
> this problem.
We need more details; what was your ptraj script and how did you specify
the reference structure. Were both the ptraj and Pymol RMS fits by mass?
-- tec3
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