[Dock-fans] Fwd: Long bonds

Mon Oct 22 13:48:40 PDT 2007

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

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Mon, 22 Oct 2007 13:37:01 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Long bonds
> To: dock-fans <dock-fans at docking.org>
> 
> 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.
> FATAL:  Atom .R<HIE 380>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 375>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 373>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 332>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 330>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 291>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 275>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 269>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 264>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 262>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 221>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 219>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 180>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 164>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 158>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 153>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 151>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 128>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 110>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<HIE 108>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 69>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<ASP 53>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<HIE 47>.A<HD1 18> does not have a type.
> FATAL:  Atom .R<ASP 42>.A<HD1 13> does not have a type.
> FATAL:  Atom .R<GLU 40>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<GLU 17>.A<HE1 16> does not have a type.
> FATAL:  Atom .R<NSER 1>.A<H 14> 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?
> 
> ----------------------------
> 
> 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:
> 
> ATOM   5140  N   THR X 333      13.448 -15.558  22.741  0.00  0.00           
> 
> ATOM   5141  H   THR X 333      12.608 -15.012  22.643  0.00  0.00           
> 
> ATOM   5142  CA  THR X 333      14.691 -14.863  22.954  0.00  0.00           
> 
> ATOM   5143  HA  THR X 333      15.655 -15.355  22.580  0.00  0.00           
> 
> ATOM   5144  CB  THR X 333      14.648 -13.582  22.114  0.00  0.00           
> 
> ATOM   5145  HB  THR X 333      15.582 -13.069  22.291  0.00  0.00           
> 
> ATOM   5146  CG2 THR X 333      14.455 -13.769  20.605  0.00  0.00           
> 
> ATOM   5147 HG21 THR X 333      14.158 -12.806  20.145  0.00  0.00           
> 
> ATOM   5148 HG22 THR X 333      15.321 -14.161  20.049  0.00  0.00           
> 
> ATOM   5149 HG23 THR X 333      13.626 -14.520  20.409  0.00  0.00           
> 
> 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           
> 
> ATOM   5157  HA  SER X 334     -17.198  20.770  11.905  0.00  0.00           
> 
> ATOM   5158  CB  SER X 334     -15.868  19.959  10.306  0.00  0.00           
> 
> ATOM   5159  HB2 SER X 334     -15.761  18.918  10.709  0.00  0.00           
> 
> ATOM   5160  HB3 SER X 334     -14.903  20.280   9.956  0.00  0.00           
> 
> ATOM   5161  OG  SER X 334     -16.906  19.973   9.300  0.00  0.00           
> 
> ATOM   5162  HG  SER X 334     -16.948  20.844   8.983  0.00  0.00           
> 
> ATOM   5163  C   SER X 334     -15.185  20.856  12.533  0.00  0.00           
> 
> ATOM   5164  O   SER X 334     -14.212  21.643  12.566  0.00  0.00 
> 
> Thanks
> francesco pietra  
> 
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