Hi,
On Thu, Feb 18, 2016 at 6:02 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
> The commend *.in file is:
> trajin 06_Prod_1ORQ_HERG_1.nc
> trajin 06_Prod_1ORQ_HERG_2.nc
> trajin 06_Prod_1ORQ_HERG_3.nc
> trajin 06_Prod_1ORQ_HERG_4.nc
> autoimage
> trajout 06_Prod_1ORQ_HERG_vmd.mdcrd
>
> It turns out at some of the frames, the protein chains are still sit in
> different cells. Does any one know which command we should use in order to
> make the protein chains always sit in the same cell?
Yikes - if your system is that voltage-dependent potassium channel
then it's a complicated beast. By default cpptraj chooses whatever the
first molecule is to be the 'anchor' molecule, but that's not always
the best choice. You can try changing the anchor to something that
should be in the 'center' - not sure what that would be offhand. If
you would like to send me off-list an example of some problem frames
(any coordinate format - restart may be best) along with the topology
I may be able to give more specific advice.
-Dan
>
> Many thanks!
>
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 18 2016 - 19:30:03 PST
