[modeller_usage] problems defining a new residue type

[barmalay alterman <>]

Hi,

I've been trying to define a new residue type
following stages a-d in
section 17 of the FAQ chapter. I have updated the
folowing *.lib files:
top,models,restyp,par,radii,radii14. Then, as a first
test I have used
align2d.top to align a pdb file that contains this new
residue with an
identical sequence, but with the residue replaced by a
standard one.

Modeller did not recognize the new residue and it
denoted it as X in 
the
pap file. I got the following warnings:

mkapsa__293W> No TOPOLOGY_LIB is in memory. Use
READ_TOPOLOGY to read 
one.
iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a
BLK residue.
              Default CHARMM atom type assigned:  N
-->  N
              This message is written only for the
first such atom.

When I included the following two lines at the
beginning of the
align2d.top file:

READ_RESTYP_LIB RESTYP_LIB_FILE= '$(LIB)/restyp.lib'
READ_TOPOLOGY FILE = '$(LIB)/top.lib', ADD_TOPOLOGY =
on

I got the following error message:

read_to_231E> CHARMM atom type is not recognized (not
in RADII_LIB):  
CR15
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1 
     1

(I got the same when the ADD_TOPOLOGY was off). But
the radii.lib file
definitely contains the relevant atoms.

I'm puzzled. Any suggestions?

Thanks a lot,
O


		
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