modeling residues with incomplete entries in the parameter library

[Yan Yao <>]

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