AMBER Archive (2006)

Subject: Re: AMBER: amber .off file format question

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon May 22 2006 - 04:16:39 CDT

I asked a question before, which was about the .off file format and did
not get any response back. I will appreciate if someone can direct me to a
website/reference/person on the description of .off (Object File Format)
file format. Thanks.

Best,

On Fri, 19 May 2006, Ilyas Yildirim wrote:

> 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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