it's not clear what you mean by "incomplete" reference.
the atoms in the pdb file need to be in the same order as those in the
trajin file. you need to have at least the first 70 residues be
complete and in the same order (since you use up to residue 70).
if you can explain better what your reference file is then we might be
able to help.
On Thu, Jan 14, 2010 at 7:29 AM, qiaoyan <qiaoyan.dicp.ac.cn> wrote:
> Dear amber users:
> I use ptraj to do rms analysis, my reference file is not complete, its residue number is 1-14 and 43-104, my script is as follows:
> trajin nptm504.dcd 1 1000 50
> reference m_addh.pdb
> rms reference ":50-70.C,CA,N" out rmsm_addh.dat time 100
> but when I check the out file, it seems extremely high, I remember the ptraj can do rms fit using incomplete file, but what is the problem I encoutered?
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Received on Thu Jan 14 2010 - 05:00:01 PST
