Subject: PM3 parameterization i

From: Pierre Mignon <[email-masked]>
Date: Fri, 31 May 2002 11:11:49 +0200 (MEST)

Hello all,

A collegue of mine gets in trouble in optimizing a peptide chain in PM3. The problem arising is that the peptide bond (O=C-N-H) is not planar in the optimized geometry. I don't mean a small deviation but the hybridation is not sp2. Does anyone has allready met this problem or has any information upon this feature ???

Thank's in advance.

Mignon Pierre
PhD student
Free University of Brussel (VUB)         
Dienst Algemene Chemie (ALGC)               
Pleinlaan, 2                            
1050 Brussels
Belgium
Tel + 32 2 629 35 16                                 
Fax + 32 2 629 33 17
e-mail [email-masked]

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From: James Robinson <[email-masked]>
Date: Fri, 31 May 2002 10:53:34 +0100

PM3 and AM1 treat amide bonds poorly. Have low rotational barriers. With Mopac93 need to add kewords MMOK to add a correction for amide bonds. 

James
-----Original Message-----
From: Computational Chemistry List [mailto:[email-masked]]On Behalf Of Pierre Mignon
Sent: 31 May 2002 10:12
To: [email-masked]
Subject: CCL:PM3 parameterization i

Hello all,

Thank's in advance.

Mignon Pierre
PhD student

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From: Per-Ola Norrby <[email-masked]>
Date: Fri, 31 May 2002 13:01:51 +0200

Hi,

>A collegue of mine gets in trouble in optimizing a peptide chain in 
>PM3. The problem arising is that the peptide bond (O=C-N-H) is not 
>planar in the optimized geometry. I don't mean a small deviation but 
>the hybridation is not sp2. Does anyone has allready met this 
>problem or has any information upon this feature ???

	This is well known.  You can get around it by adding a 
molecular mechanics term to PM3, but in fact, unless you really need 
the orbitals, almost every property is more accurately calculated if 
you use well-parameterized molecular mechanics.  There are several 
dozen methods out there that are more accurate than PM3 for peptides, 
not to mention about 3 orders of magnitude faster...

	/Per-Ola Norrby
-- 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Dept. of Chem., Org. Chem.
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: [email-masked]  tel +45-45252123,  fax +45-45933968