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 - 09:30:03 PDT
