Hi
Can you try to upgrade to ambertools 17?
V12.4 is very outdated
On Fri, Aug 4, 2017 at 5:19 PM Christopher Gorman <cbgorman.ncsu.edu> wrote:
> 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%
>
> --
> ------------------------------------------------------------------
> 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 - 15:00:02 PDT
