Dear professor:
Actually, I get my m_in.pdb file according to your instruction, but the result is still very different.
2009-11-15
qiaoyan
发件人： Thomas Cheatham
发送时间： 2009-11-15 00:27:39
收件人： qiaoyan.dicp.ac.cn; AMBER Mailing List
抄送：
主题： Re: Re: [AMBER] the different RMSD?
> trajin nptm501.dcd 1 1000 20
...
> trajout 10ns.dcd
> reference m_in.pdb
> rms reference out rms.dat ":1-104.C,CA,N" time 40
Is there a 1-1 mapping in the names between m_in.pdb and your prmtop/
generated PDB's, or in other words does atom 100 in m_in.pdb correspond to
atom 100 in the prmtop? Often the atom ordering in the input PDB
(presumably from experiment or another program) is not preserved when you
build the topology/coordinates. Try using your topology/coordinates to
build a corresponding PDB with the expected atom ordering.
Alternatively, try:
rms first out rms.dat ":1-104.C,CA,N" time 40
--tec3
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Received on Sat Nov 14 2009 - 18:30:02 PST
