Hi,
It sounds like what you want is to calculate RMSD to a reference
structure. To do this load a reference structure prior to using the
'rms' command:
reference ref.crd
rms reference mass out polyAT_vac_md1_12Acut.rms time 0.1
-Dan
On Fri, Sep 6, 2013 at 8:57 PM, 김준기 <1ruwayo.gmail.com> wrote:
> Hi
> I am bachelor and tried to calculate rmsd about trajectory of remd.
> In order to calculate rmsd, I looked at amber tutorial about rmsd.
> but what I want to calculate is not in your tutorial rmsd.
> I hope that not first structure but native structure that I downloaded in
> www.pdb.org ( not calculate the minimization).
>
> Could you tell me that what to do?
>
> Sincerely,
>
> Choonki Kim
>
>
> The precise parameter we will be calculating in this example is the mass
> weighted RMSd fit between each successive structure and the *first
> structure of our trajectory.* This is done by providing an input file to
> ptraj containing a list of commands describing the relevant files and what
> we want it to do etc.:
>
> trajin polyAT_vac_md1_12Acut.mdcrd
> rms *first* mass out polyAT_vac_md1_12Acut.rms time 0.1
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Sep 06 2013 - 21:00:02 PDT
