Re: [AMBER] dimer rmsd issue.

From: Daniel Roe <>
Date: Tue, 16 May 2017 11:16:36 -0400


On Sun, May 14, 2017 at 1:13 PM, Saman Yousuf ali
<> wrote:
> Dear All,I have plotted dimer rmsd using following command;
> parm *.prmtop
> trajin md_simulation?.mdcrd
> trajin md_simulation??.mdcrd
> autoimage
> strip :Na+,WAT outprefix nowater
> rms first out rmsd.dat :1-534.C,CA,N
> trajout netcdf

This is likely an imaging issue. When this happens to autoimage it's
usually because the default anchor choice (the first molecule) does
not really represent the "center" of your system. You should visually
inspect your system and choose a residue (or a few residues) which are
near the middle of your dimer interface as your anchor. So for example
if residues 123 and 245 are near the center of your dimer interface:

autoimage anchor :123,245

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue May 16 2017 - 08:30:03 PDT
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