Dear Amber experts,
I need to do some analysis on trajectory files. Principally, I want to generate PDB files out from a trajectory file and do some analysis on them and later combine back the PDB files to become a single trajectory file as before.
For testing the above idea, I have tried with only two frames ( each frame for each PDB file) from a trajectory file.
As a first step I have tried to generate two PDB files from a single trajectory (mdcrd) file which contain thousands of frames, using PTRAJ (from AmberTools-1.4).
As the second step I tried to combine both the PDB files (which have been generated earlier) to get a single trajectory (mdcrd) file.
The issue that I would like to inquire here is about the dimensions of the BOXES.
It looks like the BOX dimension at the first step is not CONSISTENT as in the second step.
This might give some problems if I want to use this dimension values for further calculation.
Here I have shown below the box dimensions ( the row with only three digits )as in the first and second steps respectively.
FIRST STEP ( box dimension before generating PDB files)
20.991 0.310 86.157 20.496 50.591 8.247 40.965 51.204 8.371 40.240
51.148 8.199 41.743 38.733 1.877 41.000 39.200 1.538 40.236 39.207
1.516 41.749 54.260 0.108 41.176 54.536 -0.626 40.627 53.818 -0.303
41.920 42.179 3.556 3.251 41.623 3.530 2.472 42.558 2.678 3.304 frame 1
44.723 1.496 5.937 44.339 1.355 6.803 44.866 0.614 5.593 52.401
86.323 2.974 52.385 85.816 3.785 51.879 85.808 2.359
56.907 87.404 48.231
4.792 5.052 8.317 5.279 4.463 8.898 5.663 5.341 7.220 6.267
4.438 7.137 6.477 6.566 7.627 5.857 7.407 7.936 7.301 6.170
8.741 7.647 7.020 9.023 7.315 7.107 6.475 8.171 6.435 6.413 frame 2
7.823 8.416 6.704 8.208 8.473 7.582 6.560 7.126 5.141 5.816
7.898 5.335 7.490 7.437 3.932 8.253 6.664 4.029 6.784 7.259
2.626 5.993 7.803 2.594 7.947 8.415 4.089 5.866 5.845 4.942
4.920 5.325 5.896 4.617 4.299 5.686 3.680 6.130 5.934 2.888
In the SECOND step ( combining two PDB files to become single trajectory file)
20.991 0.310 86.157 20.496 50.591 8.247 40.965 51.204 8.371 40.240
51.148 8.199 41.743 38.733 1.877 41.000 39.200 1.538 40.236 39.207
1.516 41.749 54.260 0.108 41.176 54.536 -0.626 40.627 53.818 -0.303 frame 1
41.920 42.179 3.556 3.251 41.623 3.530 2.472 42.558 2.678 3.304
44.723 1.496 5.937 44.339 1.355 6.803 44.866 0.614 5.593 52.401
86.323 2.974 52.385 85.816 3.785 51.879 85.808 2.359
104.140 159.533 88.303
4.792 5.052 8.317 5.279 4.463 8.898 5.663 5.341 7.220 6.267
4.438 7.137 6.477 6.566 7.627 5.857 7.407 7.936 7.301 6.170
8.741 7.647 7.020 9.023 7.315 7.107 6.475 8.171 6.435 6.413 frame 2
7.823 8.416 6.704 8.208 8.473 7.582 6.560 7.126 5.141 5.816
7.898 5.335 7.490 7.437 3.932 8.253 6.664 4.029 6.784 7.259
2.626 5.993 7.803 2.594 7.947 8.415 4.089 5.866 5.845 4.942
4.920 5.325 5.896 4.617 4.299 5.686 3.680 6.130 5.934 2.888
I am quite curious how to overcome this issue. Is there any technical part I need to do the get rid of this differences in the BOX dimensions?
Many thanks in advance.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Sat Mar 19 2011 - 15:00:03 PDT
