Subject: RE: Problem with iodine in GRID

From: "Teran Castañon, Hugo Gutierrez de"<[email-masked]>
Date: Fri, 25 Oct 2002 10:59:06 +0200

Dear Nikolaus,

This is what I found in GRID manual about your error:

(N970-W)  SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND NEIGHBOURS, OR THE
NUMBER OF NEIGHBOURS ONE PLACE REMOVED FROM HETATM .......
When Programme GRIN computes the positions of the hydrogen atoms on a HETATM
in the Target molecule, it starts by identifying all the other HETATMS which
are bonded to that HETATM.  It will need to know the positions of some of
these nearby HETATMS in order to calculate the hydrogen- positions, but it
sometimes does not find the expected number of neighbours.  This error
message will then be printed.

Message N970 often indicates that the structure of the Target molecule is
unusual, or that it is strained, or that it is a transition state.  GRID is
not calibrated for highly strained molecules or transition states, but we
would be grateful at Molecular Discovery if can let us know when this
message is given for a regular atom in a regular molecule

Another possibility is that the structure is wrong, or that an error has
been introduced into Datafile GRUB, or that the name of a HETATM is
incorrect, or that the molecule name, number or chain identifiers have been
misassigned.  These possibilities should be checked.

Or, in other words, that if you checked your structure and think it is ok,
you better send an e-mail to  [email-masked]

Regards,
Hugo

-----Original Message-----
From: Nikolaus Stiefl
To: [email-masked]
Sent: 10/24/2002 7:26 PM
Subject: CCL:Problem with iodine in GRID

Sorry, forget the subject. Hope this is now better.

Hi, 

I am currently investigating a set of molecules of which two contain an
iodine 
atom covalently bound to an aromatic ring. When running this dataset
through 
GRID everything works fine except for the iodine containing structures.
For 
both of them i get the following error message: 

(N970-W)  SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND 
               NEIGHBOURS, OR THE NUMBER OF NEIGHBOURS ONE PLACE 
               REMOVED FROM HETATM:      8*    8  I   <1>     1 

Now, I checked the GRID-readable pdb file and it looks o.k to me.
Therefore I 
just build iodbenzole in SYBYL (saved as mol2) and tried this with GREAT
as 
well as GREATER which results again in the mentioned error message. To
me the 
converted pdb file looks o.k. again :-(( 

I am sure someone already used GRID on iodine containing molecules so I
hope 
this someone might be able to help me ... 

Cheers 
Nik
 
----------------------
Nikolaus Stiefl
Chemometriks and Drug Design
University Wuerzburg
Dept. of Pharmacy
Am Hubland
D-97074 Wuerzburg
Germany
Phone: +49 - 931 8885473

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