[modeller_usage] HSE residue type problems

[Oliver Hucke <>]

Dear modellers,

I am trying to build an all atom protein model. Therefore I did an 
analysis of the Histidine types in my template structure and assigned 
the types HIS, HSE and HSP to the template and the conserved residues in 
the target sequence.

When I try to model the protein with HSE residues I get the following 
warnings for each HSE:

iatmcls_286W> MODEL atom not classified:  HSE:N  HSE
iatmcls_286W> MODEL atom not classified:  HSE:CA  HSE
iatmcls_286W> MODEL atom not classified:  HSE:NE2  HSE
iatmcls_286W> MODEL atom not classified:  HSE:CD2  HSE
iatmcls_286W> MODEL atom not classified:  HSE:ND1  HSE
iatmcls_286W> MODEL atom not classified:  HSE:CG  HSE
iatmcls_286W> MODEL atom not classified:  HSE:CE1  HSE
iatmcls_286W> MODEL atom not classified:  HSE:CB  HSE
iatmcls_286W> MODEL atom not classified:  HSE:C  HSE
iatmcls_286W> MODEL atom not classified:  HSE:O  HSE

Finally the calculation is terminated with the error message (see also 
below).

getdata_289_> Proteins (all/accepted):        1        1
irestab_402W> ires, irestp:       85       26
getpdf__392E> Your library requires all bins zero; nbinx:        5
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

This is not the case if I change all the HSE's in the target sequence 
(one letter code '6') to HIS ('H').

Can some body give me a hint what is going on here?

Your help is very much appreciated!

Oliver

---------------------------------------------------------------------
----- the last section of the log file with the final error message:

TOP_________>   157  118 MAKE_RESTRAINTS RESTRAINT_TYPE = 
'phi-psi_binormal', ADD_;
                      RESTRAINTS = ON


Dynamically allocated memory at        amprmcns [B,kB,MB]:     30686337 
  29967.125    29.265
make_re_417_> Restraint type to be calculated:  phi-psi_binormal
openf5__224_> Open       11  OLD  SEQUENTIAL 
${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open       11  OLD  SEQUENTIAL 
${MODINSTALL6v2}/modlib/mnch1.bin
initmdt_400_> Distance function type:        1
openf5__224_> Open       11  OLD  SEQUENTIAL 
${MODINSTALL6v2}/modlib/mnch1.mdt
irddata_401_> USER SYMMETRY, SYMMETRY:        1  T
              SYMMETRIC = .T. ==> NALN*NALN/2
              SYMMETRIC = .F. ==> NALN*NALN
              All protein pairs always generated.
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 
       1      416  HSE
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 
       1      417  PHE
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 
       3      417  PHE
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 
       4      417  PHE
getdata_643_> Protein accepted:  rat
getdata_289_> Proteins (all/accepted):        1        1
irestab_402W> ires, irestp:       85       26
getpdf__392E> Your library requires all bins zero; nbinx:        5
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

--
_______________________________________

Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific St
Seattle, WA 98195
T:(206)685-7046
_______________________________________