Hi,
You can test mask selections in cpptraj with the "parminfo" or
"select" commands. This is easiest to do in interactive mode. For
example:
> parminfo :7
#Atom Name #Res Name #Mol Type Charge Mass
105 N 7 GLY 1 N -0.4157 14.0100
106 H 7 GLY 1 H 0.2719 1.0080
107 CA 7 GLY 1 CT -0.0252 12.0100
108 HA2 7 GLY 1 H1 0.0698 1.0080
109 HA3 7 GLY 1 H1 0.0698 1.0080
110 C 7 GLY 1 C 0.5973 12.0100
111 O 7 GLY 1 O -0.5679 16.0000
> parminfo .CA
#Atom Name #Res Name #Mol Type Charge Mass
5 CA 1 SER 1 CT 0.0567 12.0100
16 CA 2 TRP 1 CT -0.0275 12.0100
40 CA 3 THR 1 CT -0.0389 12.0100
54 CA 4 TRP 1 CT -0.0275 12.0100
78 CA 5 GLU 1 CT 0.0397 12.0100
93 CA 6 ASN 1 CT 0.0143 12.0100
107 CA 7 GLY 1 CT -0.0252 12.0100
114 CA 8 LYS 1 CT -0.2400 12.0100
136 CA 9 TRP 1 CT -0.0275 12.0100
160 CA 10 THR 1 CT -0.0389 12.0100
174 CA 11 TRP 1 CT -0.0275 12.0100
198 CA 12 LYS 1 CT -0.2400 12.0100
> select .CA
Selected 12 atoms.
Selected= 5 16 40 54 78 93 107 114 136 160 174 198
You can also test mask selections in parmed.py and with ambmask.
Hope this helps,
-Dan
On Thu, Aug 8, 2013 at 2:44 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
> Hello, I am wanting to use cpptraj for some distance analysis (using the distance command). I want to see how far my ligand is from a specific residue. What is a good way for me to pick one residue, and to be certain that it is the residue I want? I know that amber numbers residues in numerical order.
>
> Thanks in advance!
> -Hunter
>
> Hunter Brown
> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
> University of New Mexico
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Thu Aug 08 2013 - 14:30:03 PDT
