Non member submission forwarded by listowner
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Date: Wed, 2 Jul 2003 09:00:22 -0700
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Subject: BOUNCE : Non-member submission from
[Aldo Jongejan <>]
From: Aldo Jongejan <>
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
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NOTE: E-mail address has changed into
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
e-mail:
tlf: +31 (0)20 4447612
fax: +31 (0)20 4447610
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