Hi,
On Thu, Mar 13, 2014 at 7:00 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
>
> angle O_P_W_angle (:322 & :POP).O (:322 & :POP).P1 ((:322 <:5.0) &
> :1140).O out O_P_W_angle_v2.txt
>
> angle O_P_W_angle (:322.O & :POP) (:322.P1 & :POP) (:322 <:5.0) &
> :1140.Oout O_P_W_angle_v2.txt
>
I think you may be over-thinking this. If you already have the residue
numbers and atom names, you are set. If you want the atom named "O" for
residue 322 just use:
:322.O
For the atom named "P" for residue 322:
:322.P
For the oxygen atom named "O" on residue 1171:
:1171.O
And so on. No need to worry about distance-based masks unless you have to.
If you haven't already, I recommend you read section "8.2.3 Atom Mask
Selection Syntax" of the AmberTools manual.
-Dan
PS - Atom masks cannot have spaces in them unless they are surrounded by
quotes; this is probably what lead to the "unbalanced parentheses" error.
--
-------------------------
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) 585-6208 (Fax)
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Received on Fri Mar 14 2014 - 07:30:03 PDT
