[Xplor-nih] HBUILD

[Gregory Zornetzer]

Hi Bryn,

Are you using the xplor-nih in python mode?  If so, I'd suggest that you
use protocol.AddUnknownAtoms() to add the MSC ligand.  HBUILD is unable to
handle adding heavy atoms, and that's the problem that you are seeing.
Addunknownatoms() basically gives random positions to every unknown atom
and then refines based on the covalent geometry.

When I was doing this, I also found that I needed to use
protocol.FixupCovalentGeometry() to really get things right.  Your mileage
may vary.

I hope this helps,
-Greg Zornetzer
gaz at nmrfam.wisc.edu

On Fri, 29 Sep 2006, R. Bryn Fenwick wrote:

>
> Hi,
>
> I am trying to build a pdb file of a molecule with a ligand attached. I
> have made the relevant topology file but can not seem to get past the
> hbuild section. I receive the below error. My ligand is named MSC. Has
> anyone else received this error or know what it might pertain to / how to
> cure the issue?
>
>
>  HBUILD: HB2 ,HB3 ,     placed for donor      410  ASN  CB  .
>  HBUILD: H   ,    ,     placed for donor      411  MSC  N   .
>  %HBUILD-ERR: Geometry unknown for donor     411  MSC  CA
>  %<HBUILD>-ERR: Unknown geometry for hydrogen donor.
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  BOMLEV=    0 reached.  Program execution will be terminated.
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  Subroutine DIE called . Terminating
>
>
> Bryn
>
>         ==========================================================
>         R. Bryn Fenwick                Department of Biochemistry,
>         rbf22 at cam.ac.uk                University of Cambridge,
>         bryn.fenwick at cantab.net        80 Tennis Court Road,
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>         Fax: +44 1223 766002           Cambridge, CB2 1GA, UK.
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