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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