AMBER Archive (2006)

Subject: AMBER: amber .off file format question

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri May 19 2006 - 21:30:55 CDT

Dear All,

I need to get a description of the .off file format, but could not find
any information in google. So here is the question:

In the .off files (Object File Format), there is an entry which has the
following line in it:

!entry.RC.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg

What does this line say? As an example, here are a couple of lines that I
took from an .off file:

 "P" "P" 0 1 131073 1 15 1.220980
 "O1P" "O2" 0 1 131073 2 8 -0.792102
 "O2P" "O2" 0 1 131073 3 8 -0.792102
 "O5'" "OS" 0 1 131073 4 8 -0.506956
 "C5'" "CT" 0 1 131073 5 6 0.038747
 "H5'1" "H1" 0 1 131073 6 1 0.075663
 "H5'2" "H1" 0 1 131073 7 1 0.075663

As far as I can understand;

name = name of the atom
type = type of the atom
typex = (No idea)
resx = res. number (!??)
flags = Dont have any clue on this. (Sometimes this is different. Here, is
        is 131073, but sometimes it is 131075, 131072, etc...)
seq = The sequence of the atoms
elmnt = element number
chg = charge of the atom

An in a particular residue .off file, do all of the atoms has to have the
SAME 'flags' number (here it is 131073)? I have created a library .off
file, which has perturbed atoms in it (atoms types are perturbed). In this
.off file, some atoms have 131073 as the 'flags' number, while some (the
ones which are perturbed) have 131075 as the 'flags' number (I followed
DAC's TI tutorial and on the second part of the tutorial when the atom
types are transformed to dummy atoms, the saved .off file has 131075 as
the 'flags' number for all of the atoms). I will appreciate if someone can
answer these questions.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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