AMBER Archive (2005)

Subject: Re: AMBER: Problem with xleap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu May 12 2005 - 18:14:38 CDT

Ok, I figured out the problem. I was using

> source leaprc.ff99

but when I changed it to

> source leaprc.rna.ff99

everything was solved.

But there is something strange happening, which I could not understand.
When my RC.pdb file was the following;

ATOM 1 P RC 1 2.314 1.777 -0.478 1.00 0.00
ATOM 2 O1P RC 1 1.933 3.073 -1.082 1.00 0.00
ATOM 3 O2P RC 1 3.157 0.872 -1.292 1.00 0.00
ATOM 4 O5* RC 1 2.994 2.142 0.923 1.00 0.00
ATOM 5 C5* RC 1 2.156 2.552 2.020 1.00 0.00
ATOM 6 1H5* RC 1 1.453 1.754 2.258 1.00 0.00
ATOM 7 2H5* RC 1 1.605 3.450 1.741 1.00 0.00
ATOM 8 C4* RC 1 3.008 2.848 3.243 1.00 0.00
ATOM 9 H4* RC 1 2.447 3.477 3.934 1.00 0.00
ATOM 10 O4* RC 1 3.228 1.605 3.977 1.00 0.00
ATOM 11 C1* RC 1 4.559 1.151 3.778 1.00 0.00
ATOM 12 H1* RC 1 5.072 1.095 4.737 1.00 0.00
ATOM 13 N1 RC 1 4.501 -0.268 3.327 1.00 0.00
ATOM 14 C6 RC 1 4.258 -0.582 2.026 1.00 0.00
ATOM 15 H6 RC 1 4.104 0.203 1.300 1.00 0.00
ATOM 16 C5 RC 1 4.206 -1.878 1.616 1.00 0.00
ATOM 17 H5 RC 1 4.010 -2.111 0.570 1.00 0.00
ATOM 18 C4 RC 1 4.416 -2.881 2.614 1.00 0.00
ATOM 19 N4 RC 1 4.379 -4.159 2.286 1.00 0.00
ATOM 20 1H4 RC 1 4.532 -4.836 3.019 1.00 0.00
ATOM 21 2H4 RC 1 4.202 -4.434 1.330 1.00 0.00
ATOM 22 N3 RC 1 4.653 -2.564 3.884 1.00 0.00
ATOM 23 C2 RC 1 4.701 -1.262 4.273 1.00 0.00
ATOM 24 O2 RC 1 4.919 -0.928 5.447 1.00 0.00
ATOM 25 C3* RC 1 4.416 3.378 2.961 1.00 0.00
ATOM 26 H3* RC 1 4.412 3.941 2.028 1.00 0.00
ATOM 27 C2* RC 1 5.230 2.096 2.779 1.00 0.00
ATOM 28 1H2* RC 1 5.668 2.081 1.781 1.00 0.00
ATOM 29 O2* RC 1 6.273 2.050 3.757 1.00 0.00
ATOM 30 2HO* RC 1 6.759 1.235 3.611 1.00 0.00
ATOM 31 O3* RC 1 5.030 4.129 3.998 1.00 0.00
TER
END

xleap was adding two atoms, HO'2 and and O2'. When the .pdb file was in
primed notation (with 's rather *s), xleap did not give any error.
Moreover, when I used the following command in xleap to create the pdb
files

> savepdb RC rc.pdb

xleap was creating a file 'rc.pdb' with the star notation. I checked out
the leaprc.ff99 file, and in that file the 'all_nucleic94.lib' library is
used for nucleic acids. And in that library, the primed notation is used.
How can xleap create a file with starred notation if that residue is
defined in primed notation? I first thought that xleap does not care
whether it is a * or ', and would realize that it is the sugar part. But
as I described above, there are some strange things happening. I think
there is a bug with this.

I think the answer to the first question lies in the atommapping. In the
leaprc.ff99 file, there is a part which is as follows:

addPdbAtomMap {
  { "O5*" "O5'" }
  { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" }
  { "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" }
  { "C1*" "C1'" }
  { "C5M" "C7" }
  { "H1*" "H1'" }
  { "H2*1" "H2'1" }
  { "H2*2" "H2'2" }
  { "H3*" "H3'" }
  { "H4*" "H4'" }
  { "H5*1" "H5'1" }
  { "H5*2" "H5'2" }
# old ff atom names -> new
  { "O1'" "O4'" }
  { "OA" "O1P" }
  { "OB" "O2P" }
}

If initially the .pdb file has 2HO* and O2*, they arent gonna be mapped to
any atom in the library. So, the library will create those atoms (2HO' and
O2'). Adding these atoms to the above atommapping might solve it. But I
still do not know why the 'savepdb RC rc.pdb' creates sugar atoms with
starred notation.

Best,

On Thu, 12 May 2005, FyD wrote:

> In some cases, LEaP add unwanted atoms for some particular residue _names_...
> Bugs ? Or even do not accept some atom names...
> Try to change the residue name/file name...
> Regards, Francois
>
> > I have a question regarding xleap. It is about the AMBER's libraries, and
> > something strange is happening when I am trying to do the following:
> >
> > I start 'xleap'. Then;
> >
> > > source leaprc.ff99
> > > savepdb RC rc.pdb
> > > quit
> >
> > Now, I see the file 'rc.pdb' in the directory. Then I start 'xleap' again;
> >
> > > source leaprc.ff99
> > > molecule = loadpdb rc.pdb
> >
> > and xleap adds 2 atoms!!! Here is what xleap is giving me after I load the
> > rc.pdb:
> >
> > > molecule = loadpdb rc.pdb
> > Loading PDB file: ./rc.pdb
> > Created a new atom named: O2* within residue: .R<RC 1>
> > Created a new atom named: HO*2 within residue: .R<RC 1>
> > Added missing heavy atom: .R<RC 1>.A<O2' 29>
> > total atoms in file: 31
> > Leap added 2 missing atoms according to residue templates:
> > 1 Heavy
> > 1 H / lone pairs
> > The file contained 2 atoms not in residue templates
> > Since added/missing = extra, there is a high probability
> > of atoms with 'incorrect' names; you may want to
> > use addPdbAtomMap to map these names, or change in file
> >
> > Question: I have saved the .pdb structure according to the AMBER' residue
> > library, and when I try to open the same .pdb in xleap, it adds two atoms
> > (saying that they are missing, even though they are not!). Am I missing
> > something here? Thanks in advance for your responses.
>
> 

-- 
  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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