Dear All,I have performed 5ns MD simulation using amber14. After that I have performed reimaging using following script;
script=======
parm complex.prmtop
trajin md_simulation1.mdcrd.gzcenter :1-267
image familiartrajout reimage-md_simulation1.mdcrd.gz
then I observed that out 0f 5000 frames only 4867 frames processed during reimaging. Output is pasted below.
CPPTRAJ: Trajectory Analysis. V12.1
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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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Received on Tue Oct 18 2016 - 03:00:02 PDT
