Non member submission forwarded by listowner

------ Forwarded Message From: owner-modeller_usage@salilab.org Date: Wed, 2 Jul 2003 09:00:22 -0700 To: modeller_usage-approval@salilab.org Subject: BOUNCE modeller_usage@salilab.org: Non-member submission from [Aldo Jongejan jongejan@few.vu.nl]

From: Aldo Jongejan jongejan@few.vu.nl

Dear readers,

I have specified a ligand for use in the modelling procedure along the lines of the answer to FAQ 17. However, I get an error:

check_ali___> Checking the sequence-structure alignment.

Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:

ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 446 1 327 334 K I 14.724 END OF TABLE

patch_s_522_> Number of disulfides patched in MODEL: 1 delete__442E> One or more atoms absent from MODEL: O: 445: C: 445: N: 446: CA: 446:

I have specified the PATC FIRS NONE LAST NONE in the top_heav.lib, so I expected this residue to be on its own and have no links to the protein. It seems that MODELLER wants to link the residue to the Cterm. How can I prevent this?

The last part of my alignment is as follows:

EHCWK------------------------------------/i*

But substituting / by - does not help either. In the PDB file for the structure the ligand is now specified forming a separate chain.

Can somebody help me with this problem??

with kind regards,

aldo