VMD-L Mailing List

From: Gamot, Ritchie (R.M.Gamot_at_warwick.ac.uk)
Date: Tue Jul 31 2012 - 06:51:52 CDT

Dear All,

good day!

i would like to be able to know how to go through all the atoms in my file and calculate the distance of it to allthe other atoms. like, get ARG1 and compute the distance to ARG2, ARG3, etc and possibly take the sum of in the end.

i also would like to determine a sort of nearest neighbor cmputation. like for example, i take ARG1, i would like to determine the atoms/points which are in a distance of dist from it. so basically if i take a sphere around an atom/point, i would like to determine the atoms that are included in that sphere. i need to do this for each atom in my molecule.

i do hope that you can help me out with this query of mine, as of now i am looking into several possible scripts that i can use from the uiuc website but hopefully if you can help me with this, i would appreciate it a lot.

thank you very much!

regards,

Chimie Gamot

i have a trajectory file in the format:

98
Frame 0
ARG1 1.23 0.79 0.45
ARG2 2.90 -1.23 0.004
.
.
ARG98 1.56 -1.43 0.89
98
Frame 1
ARG1 0.23 2.79 -0.45
ARG2 -1.90 -2.23 3.004
.
.
ARG98 1.43 -1.27 0.12
etc
etc
etc

and i have another reference file of the format:

98
Reference
ARG1 2.23 1.79 -0.45
ARG2 -1.90 2.23 1.004
.
.
ARG98 1.34 -2.43 1.29