[Dock-fans] amberize_rec.out error

Scott Brozell sbrozell at scripps.edu
Mon Mar 5 22:10:54 PST 2007


Hi,

Sorry for the slow reply.

On Fri, 23 Feb 2007, Gustavo HMF Souza wrote:

> I see this error when I try to run ./prepare_amber.pl on 1O8A.pdb file. I
> already apply sed change the HIS to HIP but appears to be improper
> torsion errors. Please look carefully the file below:
...
> Loading PDB file: ./1O8A.pdb
>   Added missing heavy atom: .R<NASP 40>.A<CG 10>
>   Added missing heavy atom: .R<NASP 40>.A<OD1 11>
>   Added missing heavy atom: .R<NASP 40>.A<OD2 12>
>   Added missing heavy atom: .R<GLU 64>.A<CG 8>
>   Added missing heavy atom: .R<GLU 64>.A<CD 11>
>   Added missing heavy atom: .R<GLU 64>.A<OE1 12>
>   Added missing heavy atom: .R<GLU 64>.A<OE2 13>
>   Added missing heavy atom: .R<LYS 117>.A<CG 8>
>   Added missing heavy atom: .R<LYS 117>.A<CD 11>
>   Added missing heavy atom: .R<LYS 117>.A<CE 14>
>   Added missing heavy atom: .R<LYS 117>.A<NZ 17>
>   Added missing heavy atom: .R<SER 298>.A<OG 8>
>   Added missing heavy atom: .R<GLU 303>.A<CG 8>
>   Added missing heavy atom: .R<GLU 303>.A<CD 11>
>   Added missing heavy atom: .R<GLU 303>.A<OE1 12>
>   Added missing heavy atom: .R<GLU 303>.A<OE2 13>
>   Added missing heavy atom: .R<LYS 307>.A<CG 8>
>   Added missing heavy atom: .R<LYS 307>.A<CD 11>
>   Added missing heavy atom: .R<LYS 307>.A<CE 14>
>   Added missing heavy atom: .R<LYS 307>.A<NZ 17>
>   Added missing heavy atom: .R<SER 435>.A<CB 5>
>   Added missing heavy atom: .R<SER 435>.A<OG 8>
>   Added missing heavy atom: .R<ASP 436>.A<CG 8>
>   Added missing heavy atom: .R<ASP 436>.A<OD1 9>
>   Added missing heavy atom: .R<ASP 436>.A<OD2 10>
>   Added missing heavy atom: .R<CGLN 614>.A<CA 3>
>   Added missing heavy atom: .R<CGLN 614>.A<CB 5>
>   Added missing heavy atom: .R<CGLN 614>.A<C 16>
>   Added missing heavy atom: .R<CGLN 614>.A<CG 8>
>   Added missing heavy atom: .R<CGLN 614>.A<O 17>
>   Added missing heavy atom: .R<CGLN 614>.A<OXT 18>
>   Added missing heavy atom: .R<CGLN 614>.A<CD 11>
>   Added missing heavy atom: .R<CGLN 614>.A<OE1 12>
>   Added missing heavy atom: .R<CGLN 614>.A<NE2 13>
>   total atoms in file: 4660
>   Leap added 4602 missing atoms according to residue templates:
>        34 Heavy
>        4568 H / lone pairs

These missing heavy atoms are consistent with the pdb record:
see remark 470 or inspect the actual residues.
This is probably ok since LEaP added the missing atoms.

> Writing pdb file: 1O8A.amber.pdb
>  Converting N-terminal residue name to PDB format: NASP -> ASP
>  Converting C-terminal residue name to PDB format: CGLN -> GLN
> Checking Unit.
> WARNING: There is a bond of 11.551531 angstroms between:
> -------  .R<SER 434>.A<C 10> and .R<SER 435>.A<N 1>

This is more problematic.  From remark 465, SER GLU GLY GLY is missing:
ATOM   3189  N   SER A 434      64.282  23.702  31.812  1.00 49.72           N
ATOM   3190  CA  SER A 434      65.552  23.375  31.173  1.00 51.10           C
ATOM   3191  C   SER A 434      65.745  24.157  29.879  1.00 51.56           C
ATOM   3192  O   SER A 434      66.428  25.182  29.860  1.00 52.18           O
ATOM   3193  CB  SER A 434      65.619  21.873  30.887  1.00 51.49           C
ATOM   3194  OG  SER A 434      64.505  21.452  30.117  1.00 52.92           O
ATOM   3195  N   SER A 439      64.653  32.326  21.785  1.00 48.10           N
ATOM   3196  CA  SER A 439      63.950  31.478  20.839  1.00 48.51           C
ATOM   3197  C   SER A 439      62.522  31.928  20.591  1.00 47.84           C
ATOM   3198  O   SER A 439      61.718  31.998  21.520  1.00 48.31           O

If this region of the receptor will be movable then you very probably
will need to add these residues; LEaP cannot automagically fix this.
On the other hand if this region is not movable then you might get
away with ignoring this.

> WARNING: The unperturbed charge of the unit: 7.000000 is not zero.
>
>  -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Building angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Building proper torsion parameters.
>  ** No torsion terms for  HS-SH-SH-CT
>  ** No torsion terms for  HS-SH-SH-HS
>  ** No torsion terms for  CT-SH-SH-CT
>  ** No torsion terms for  CT-SH-SH-HS
>  ** No torsion terms for  HS-SH-SH-CT
>  ** No torsion terms for  HS-SH-SH-HS
>  ** No torsion terms for  CT-SH-SH-CT
>  ** No torsion terms for  CT-SH-SH-HS
>  ** No torsion terms for  HS-SH-SH-CT
>  ** No torsion terms for  HS-SH-SH-HS
>  ** No torsion terms for  CT-SH-SH-CT
>  ** No torsion terms for  CT-SH-SH-HS
> Building improper torsion parameters.
>  total 1968 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>     Quit

Specific comments:
These messages are symptomatic of incorrectly labeled cysteine residues.
In particular, the pdb file needs to be edited to change cysteine
residue names involved in disulfide bonds from CYS to CYX.
(The missing parameter messages all involve hydrogen bonded to sulfur,
and once LEaP recognizes that a sulfur-sulfur bond exists then the hydrogens
will not exist and there will be no need for the missing parameters,
but see below.)

General advice and comments:
If disulfide bonds are important then verify that the pdb file contains
correct conect records for them.  (There are other ways to handle
disulfide bonds in Amber, but the DOCK Amber score preparation scripts
are not designed to use those alternate mechanisms; see section 1.4 and
page 13 of the Amber 9 Manual http://amber.scripps.edu/doc9/amber9.pdf .)

I'll add some comments on disulfide bonds to the Amber score tutorial.

Scott



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