Hi,
Can you send me off-list the trajectory frame in question (number 11)
along with the corresponding topology file so I can try to reproduce
what you are seeing? Also, what version of cpptraj are you using
(cpptraj --version)? Thanks.
-Dan
On Tue, Feb 2, 2016 at 2:28 AM, A kS <aks25121986.gmail.com> wrote:
> Dear AMBER user,
>
> I am using *mask command* in *cpptraj of AT14* to:
>
> <1> I want to know the *atoms that are within the 4A from the oxygen atom
> of a water molecule* (WAT.O) (solvent mask :158)* for a particular frame*
> in an *autoimaged trajectory* as :
>
> trajin autoimaged.mdcrd 11 11
> strip :158.H*
> mask "(:158<:4)&!:158" maskout mask.out
>
> *MY PROBLEM IS*:
>
> When I calculate the *distance between the atoms* that are coming out from
> the mask command and the :158.O for that particular frame as :
>
> trajin autoimaged.mdcrd 11 11
> distance :158.O .58 out dist_11_58.dat
>
> *I have found some of the distance >4A even upto 34A.*
>
> I think this should not be happens but I am unable to identify the problem.
>
> Regards
> Aks
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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 Tue Feb 02 2016 - 07:30:04 PST
