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Error on reading ligands



Non member submission forwarded by listowner

------ Forwarded Message
From: 
Date: Wed, 2 Jul 2003 09:00:22 -0700
To: 
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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