Dear Wei,
Thanks a lot for the useful information. The reason why I am asking
this question is because of some library files I created before. These
.off library files have 131075 as the flags number for some atoms. The
atoms which have this flags number are perturbed atoms. Here, I have to
note one thing: When only the charge is perturbed, the atom is seen as
UNPERTURBED in xleap when the desc command is used. When the atom changes
its TYPE, then it is seen as perturbed. As a result, those atoms which
have ATOM TYPE perturbation, their flag number is 131075 in the .off
files rather 131072. And this is very important while creating the prmtop
files in xleap.
If the flag number of the perturbed atoms are changed from 131075 to
131072 (which I did before, because I did not think that it was
important), the saved prmtop file is different. And as a result, the
simulation is giving wrong results.
It will be very useful to include an explanation of the .off files,
because we write a lot of scripts and in some of the scripts, we use these
.off files to create some other file formats (at least I am doing this).
Thanks a lot again Wei. Best,
On Mon, 22 May 2006, Wei Zhang wrote:
> 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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>
--
Ilyas Yildirim
---------------------------------------------------------------
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Received on Wed May 24 2006 - 06:07:13 PDT
