AMBER Archive (2006)

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

From: Wei Zhang (zweig_at_scripps.edu)
Date: Mon May 22 2006 - 13:13:12 CDT

Hi,

I think I have a clue about it.

First, about the flags. In xleap, run desc on
an atom you will get:

.........
........
atom flags: 20000 | posfxd- posblt- sel- pert-
notdisp- tchd- posknown+ int- nmin- nbld-

It is the definition of atom flag, here
20000 is in hex format, in dec format it
shoule be 131072. that is why most atoms'
flag is 131072. and the following is what the
flags mean, according to the source code:

posfxd: position fixed
posblt: position built
posdrwn: position drawn
sel,selected: atom selected
pert: atom perturbed
notdisp: atom not displayed
touched: atom touched
posknwn: posiition known
int, internal: internal position
nmin, needsmin: need minimize
nbld, needsbld: need bulid

my current understanding is these flags are only used
by leap itself

Typex is supposed to be type index, which should be
an distinguish number for each atom type. but it seems
the author found it is too tedious to do that, so currently
it is set to zero for every atom.

and yes resx is the residue number.

I hoped it is useful. May I ask you why do you need this
information? since I am preparing a new version of leap,
I want to know users' interest.

Sincerely,

Wei

Ilyas Yildirim wrote:

>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,
>>
>>
>>
>>
>
>
>

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