[Dock-fans] Fwd: Long bonds

[Scott Brozell]

Hi,

On Mon, 22 Oct 2007, Francesco Pietra wrote:

> Sorry, forgot: how to recognize where the protons are on histidine, so that
> HIE can be changed to HID? Similarly for aspartic.

I probably do not understand the question; did you examine the 
structures in a visualizer, such as Chimera, VMD, etc.
See the Amber score tutorial or the Amber manual for the definition
of HID, HIE, etc.
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
See below.

> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> 
> > With my large protein and ligand I was able to carry out docking, both rigid
> > and flex ligand. Amber_score failed because of two kinds of problems with the
> > protein.

> > 1st PROBLEM (protons on histidine, etc): 
> > FATAL:  Atom .R<GLU 443>.A<HE1 16> does not have a type.
> > FATAL:  Atom .R<HIE 441>.A<HD1 18> does not have a type.
> > FATAL:  Atom .R<ASP 402>.A<HD1 13> does not have a type.
> > FATAL:  Atom .R<ASP 386>.A<HD1 13> does not have a type.

> > Is that better in such cases to edit the names by hand (problematic with
> > aspartic, H on O), or make recourse to (a) downlodable sourceforge softw, (b)
> > "biophysics" softw on server?

The appropriate method depends on several factors including your
confidence in the existing protonation versus your confidence
in those produced by tools, as well as whether the existing proton
states/coordinates need to be preserved.  See these for additional comments:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000892.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-January/000876.html

> > ----------------------------

> > 2nd PROBLEM:

> > WARNING: There is a bond of 50.040630 angstroms between: 
> > -------  .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
> > WARNING: There is a bond of 39.464740 angstroms between: 
> > -------  .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
> > WARNING: There is a bond of 49.372740 angstroms between: 

> > I was advised to insert "TER" records between the residues that the bond is
> > connecting. For the first long bond, is that correct as follows:

The central issue is whether there should be a bond between these
residues ?  If not then insert TER cards after each separate
molecule.  If there should be a bond then the initial xyz coordinates
are screwed up.

Scott

...
> > ATOM   5150  OG1 THR X 333      13.670 -12.723  22.556  0.00  0.00           
> > ATOM   5151  HG1 THR X 333      12.831 -13.194  22.522  0.00  0.00           
> > ATOM   5152  C   THR X 333      14.755 -14.634  24.443  0.00  0.00           
> > ATOM   5153  O   THR X 333      15.694 -15.150  25.132  0.00  0.00 
> > TER           
> > ATOM   5154  N   SER X 334     -16.176  22.312  10.940  0.00  0.00           
> > ATOM   5155  H   SER X 334     -15.301  22.760  10.966  0.00  0.00           
> > ATOM   5156  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00           
...