Hi, I'm trying to compute the radial distribution function (RDF) of
selected atoms in the dendrimer with respect to the center of mass in the
molecule. I have executed the cpptraj commands below, but the program just
hangs (non-responsive for > 15 min). I think I have the correct syntax but
I guess not. Can anybody help me out?
Also, what is "imaging"? I can't find a definition in the ambertools
manual.
[cbgorman.login03 cbgorman]$ cpptraj
CPPTRAJ: Trajectory Analysis. V12.4
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> parm G3-dox-OH.prmtop
[parm G3-dox-OH.prmtop]
> trajin G3-dox-OH-prod-nice.crd
[trajin G3-dox-OH-prod-nice.crd]
[G3-dox-OH-prod-nice.crd] contains 100 frames.
> strip :WAT
[strip :WAT]
> radial G2.rdf 0.5 20 :* :6-13.N4 center1
[radial G2.rdf 0.5 20 :* :6-13.N4 center1]
> go
INPUT TRAJECTORIES:
[G3-dox-OH-prod-nice.crd] is an AMBER trajectory, Parm 0 (reading 100 of
100)
Coordinate processing will occur on 100 frames.
PARAMETER FILES:
0: G3-dox-OH.prmtop, 29388 atoms, 9389 res, ortho. box, 9329 mol, 9328
solvent mol, 100 frames
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 2 actions:
0: [strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
1: [radial G2.rdf 0.5 20 :* :6-13.N4 center1]
RADIAL: Calculating RDF for atoms in mask [:*] to atoms in mask
[:6-13.N4]
Output to G2.rdf.
Using center of atoms in mask1.
Histogram max 20.000000, spacing 0.500000, bins 40.
Normalizing using particle density of 0.033456 molecules/Ang^3.
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [G3-dox-OH.prmtop]: Setting up 2 actions.
0: [strip :WAT]
Stripping 27984 atoms.
strip.G3-dox-OH.prmtop: Setting up 1423 bonds.
Topology contains 1404 atoms.
61 residues.
1423 bonds.
1 molecules.
1: [radial G2.rdf 0.5 20 :* :6-13.N4 center1]
RADIAL: 1404 atoms in Mask1, 8 atoms in Mask2, Imaging on.
----- [G3-dox-OH-prod-nice.crd] (1-100, 1) -----
0%
--
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Christopher Gorman, Professor of Chemistry
Department of Chemistry 919-515-4252 (office)
North Carolina State University 919-515-8920 (fax)
Box 8204 919-515-8918 (lab)
Raleigh, NC 27695-8204 Chris_Gorman.ncsu.edu
Use 45 Dabney Hall instead of Box 8204 for Express Deliveries
Learn about the Gorman group on the WEB:
http://www4.ncsu.edu/~cbgorman
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Received on Fri Aug 04 2017 - 14:30:02 PDT
