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 [email protected] 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, > [email protected] University of Cambridge, > [email protected] 80 Tennis Court Road, > Tel: +44 1223 766018 Old Addenbrookes Site, > Fax: +44 1223 766002 Cambridge, CB2 1GA, UK. > ========================================================== > _______________________________________________ > Xplor-nih mailing list > [email protected] > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >
