hello all,

I am modeling a set of mutants of cytochrome c using structure of cytochrome c from horse heart as template. the alignment is as such:

>P1;1akk structureX:1akk: 1 : : 105 : :oxidized cytochrome c:horse heart: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYI PGTKMIFAGIKKKTEREDLIAYLKKATNE/h*

>P1;1aaa sequence:1aaa: 1 : : 105 : :cytochrome c:rat: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKY IPGTKMIFAGIKKKGERADLIAYLKKATNE/h*

the model script is: Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE # Include the predefined TOP routines

SET ALNFILE = 'alignment2.ali' # alignment filename SET KNOWNS = '1akk' # codes of the templates SET SEQUENCE = '1aaa' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET OUTPUT_CONTROL = 1 0 0 1 SET HYDROGEN_IO = on SET HETATM_IO = on SET WATER_IO = on SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' SET GENERATE_METHOD = 'transfer_xyz' SET TOPOLOGY_MODEL = 1 SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model

the hetatm, water, hydrogen options were set on, the generate_method is as 'transfer_xyz', which is hoped to define the model coordinates before calling MAKE_RESTRAINTS according to the manual on "modeling residues with non-existing or incomplete entries in the topology and parameter libraries. but it kept on giving the __E strings in the log file as below which suggest the heme group has missing parameters..

addcr___E> cannot find params in params file: CHARMM atoms: NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B atom indices: 1637 1636 1638 1645 residues : HEME HEME HEME HEME addprm__W> Adding params (mean,force,period) -10.78135 10.00000 3 for atoms $

I already tried the modeller6a version but does not help.. any suggestions would be greatly appreciated.

Yan