Dear Daniel,
Thank you very much. The image files works very nice after using anchor.
Best regards,
Catherine
> Date: Tue, 31 Jul 2012 10:22:31 -0600
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] After autoimage, rms jump
>
> Hi,
>
> On Tue, Jul 31, 2012 at 1:17 AM, Catein Catherine
> <askamber23.hotmail.com> wrote:
> > However, how to do it? I found "Error: Anchor mask [:100-200] corresponds to 0 mols, should only be 1." when I use the
> > autoimage :100-200
>
> You were on the right track. Currently autoimage with no arguments
> centers by default on the first molecule in your system. When that
> molecule is not the one that takes up the largest amount of space in
> the box you can still get imaging artifacts (as you discovered). The
> 'anchor' mask when specified should incorporate all atoms of the
> molecule you want to anchor on. In your case this is residues 37 to
> 460. So this input should work for you:
>
> parm D1_wat.prmtop
> trajin md35.mdcrd
> autoimage anchor :37-460
> rms first out rmsd.dat .CA,C1'
>
> Future incarnations of autoimage will anchor the largest molecule by
> default. Thanks for the report, let me know if there is anything else
> I can help with.
>
> -Dan
>
> --
> -------------------------
> 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 Tue Jul 31 2012 - 20:30:03 PDT
