From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Wed Jul 27 2005 - 04:41:06 CDT
Here's something I prepared a while back for my own
reference on the basis of the pdb file format
specification. I'll paste it into the email, but I
suggest looking at the attached file as the formatting
is bound to get messed up.
1 2 3 4 5
6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540
1.00 11.92 A1 N
| | | || || | | | |
| | | | |
N n n a r c r i x y z
O B s e c
a r a l e h e c
e l h
m m t s a s o
g e r
e e l n i n d
I m g
o a n r e
D t e
c m I
e D
COLUMNS DATA TYPE FIELD
DEFINITION
---------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom
serial number.
13 - 16 Atom name Atom
name.
17 Character altLoc Alternate
location indicator.
18 - 20 Residue name resName Residue
name.
22 Character chainID Chain
identifier.
23 - 26 Integer resSeq Residue
sequence number.
27 AChar iCode Code for
insertion of residues.
31 - 38 Real(8.3) x
Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) y
Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) z
Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) occupancy
Occupancy.
61 - 66 Real(6.2) tempFactor
Temperature factor.
73 - 76 LString(4) segID Segment
identifier, left-justified.
77 - 78 LString(2) element Element
symbol, right-justified.
79 - 80 LString(2) charge Charge on
the atom.
--- Wei Chen <gtg553p_at_mail.gatech.edu> wrote:
> Hi Deborah,
>
> I didn't notice that before. But I think the order
> is important. I guess
> namd reads pdb files in for strings and then
> transfers different regions into
> corresponding data.
>
> Does anybody have comments on this?
>
> Wei
>
>
> Quoting Deborah Jameson <debyjameson_at_yahoo.com>:
>
> > Dear Wei
> >
> > I noticed the the function of B colomn, but what I
> mentioned is that the
> > space number between two colomns interfere in the
> results which are given in
> > fepout file. for example if you transfer all data
> in a colomn by one or two
> > space to right or left then you will see that the
> results differ.
> > This means that fep file should follow a specific
> order so that the results
> > be reliable.
> > this holds also when moving the minus sign by one
> space and the results
> > change very much.
> >
> > Thanks again
> > Best Regards,
> > Deb
> >
> > Wei Chen <gtg553p_at_mail.gatech.edu> wrote:
> > Hi, Deborah,
> >
> > I don't understand what exactly you mean. Because
> we use B colomn to
> > indicate status of each atom (fepCol B), A value
> of -1 in B column indicates
> > the atom will vanish during the FEP calculation,
> whereas a value of 1
> > indicates
> > that the atom will grow and 0 means invariant.
> According your needs, you
> > can set those values.
> >
> > Regards,
> >
> > Wei
> >
> > Quoting Deborah Jameson :
> >
> > > Hi Wei
> > >
> > > I really appreciate your giving useful
> instructions and also the files
> > which
> > > helped me very much in preparing my model.I
> could build the psf,pdf conf
> > and
> > > fep files for zero-sum ethane to ethane which is
> mentioned in fep manual.
> > > after running the model,I found out that the
> results are very sensitive to
> > > the positions of colomns of data in fep
> file(specially the B colomn) and
> > > results vary very much with changing the
> position of this colomn or other
> > > colomns or even one data(e.g. -1 in B colomn).
> > > I am really uncertain about the results and want
> to ask if you know how it
> > is
> > > possible to be sure about the validity of the
> results.
> > > I have attached the files. would you please take
> a look at them and check
> > how
> > > significantly the results will change by
> changing the positions of data in
> > > fep file.(for example just moving -1 in B colomn
> or just moving U colomn).
> > > have you faced this problem yet? it is really
> dangerous to rely upon the
> > > results when they change with simple changes in
> the data positions in fep
> > > file.(in the manual the results are given which
> are different from mine)
> > >
> > > Thank you very much for your consideration again
> > > Best Wishes
> > > Deb
> > >
> > >
> > >
> > >
> > >
> __________________________________________________
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> > > Tired of spam? Yahoo! Mail has the best spam
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> >
> >
> > --
> >
> >
> > __________________________________________________
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>
> --
>
>
>
___________________________________________________________
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1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 A1 N
| | | || || | | | | | | | | |
N n n a r c r i x y z O B s e c
a r a l e h e c e l h
m m t s a s o g e r
e e l n i n d I m g
o a n r e D t e
c m I
e D
COLUMNS DATA TYPE FIELD DEFINITION
---------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
73 - 76 LString(4) segID Segment identifier, left-justified.
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.
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