Hi,
Cpptraj version 12.1 is 4 years old at this point (and is not even the
most patched version of 12!). I recommend upgrading to AmberTools 16.
If there is a problem it may have been fixed since then.
On Tue, Oct 18, 2016 at 5:44 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
>
> then I observed that out 0f 5000 frames only 4867 frames processed during reimaging. Output is pasted below.
Can you visualize the output trajectory? Does it seem to be corrupted
in any way?
-Dan
>
> CPPTRAJ: Trajectory Analysis. V12.1
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from file reimage.in
> [trajin md_simulation1.mdcrd.gz]
> [md_simulation1.mdcrd.gz] contains 5000 frames.
> [trajout reimage-apo_4cm6-Achain.mdcrd]
> [center :1-267]
> [image familiar]
>
> INPUT TRAJECTORIES:
> [md_simulation1.mdcrd.gz] is an AMBER trajectory, Parm 0 (with box info) (reading 5000 of 5000)
> Coordinate processing will occur on 5000 frames.
>
> PARAMETER FILES:
> 0: 4cm6-apo-Achain.prmtop, 36437 atoms, 11068 res, ortho. box, 10802 mol, 10794 solvent mol, 5000 frames
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> [reimage-apo_4cm6-Achain.mdcrd] is an AMBER trajectory, Parm 0: Writing 5000 frames
>
> ACTIONS: Initializing 2 actions:
> 0: [center :1-267]
> CENTER: To box center via center of geometry using atoms in mask :1-267
>
> 1: [image familiar]
> IMAGE: To box center based on first atom position using atoms in mask *
> Triclinic On, familiar shape.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [4cm6-apo-Achain.prmtop]: Setting up 2 actions.
> 0: [center :1-267]
> :1-267 (3976 atoms)
> 1: [image familiar]
> Number of molecules to be imaged is 10802 based on mask [*]
> ----- [md_simulation1.mdcrd.gz] (1-5000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
> Read 4867 frames and processed 4867 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> There are no data sets set up for analysis.
> Kindly help me to figure out this issue
> Thanks. Best, Saman Yousuf Ali
> _______________________________________________
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Oct 18 2016 - 06:00:04 PDT
