Subject: R-C=C-R atom type

From: "Emadeddin Tajkhorshid" <[email-masked]>
Date: Thu, 26 Feb 1998 11:21:17 -0800

Dear CCLers

I have a ligand which contains two conjugated doule bonds in its dtructure.

R-C=C-C=C-R

I am wondering for the proper atom type for the SP2 carbons and their hydrogens
in AMBER. Is there any explicit atom type for these atoms or do I have to
consider one of the available SP2 carbons which is normally used for the
aromatic rings or carbonyl group?

Thanx

-- 
Emad
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E. Tajkhorshid				
German Cancer Research Center; DKFZ             Tel: +49 6221 42 2340
Dept. Molecular Biophysics (0810)               FAX: +49 6221 42 2333
P.O.Box 101949			   
69009 Heidelberg, FRG         Email: [email-masked] 
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* "Never express yourself more clearly than you think." -Niels Bohr *
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From: Pieter Stouten <[email-masked]>
Date: Thu, 26 Feb 1998 10:23:20 -0500

On 98/02/26 at 11:21 -0800, Emadeddin Tajkhorshid wrote:

>I am wondering for the proper atom type for the SP2 carbons and their
>hydrogens in AMBER. Is there any explicit atom type for these atoms or
>do I have to consider one of the available SP2 carbons which is normally
>used for the aromatic rings or carbonyl group?
>
Sounds like the poly-ene problem. Typically, these systems are not aromatic
and then there is a length difference between the single and double bonds.
If all the carbons have the same atom type, then there is no way to
distinguish between the single and double bonds. There are two principle
solutions (but I have no clue how Amber might handle this):

1) using alternating atom types for adjacent carbon pairs (e.g.
   -Cx=Cx-Cy=Cy-Cx=Cx-Cy=Cy etc.) and use identical (double bond) lengths
   and force constants for "like" atom pairs Cx=Cx and Cy=Cy and different
   (single bond) lengths and force constants for "unlike" pairs Cx-Cy.
2) using explicit bond orders as is done e.g. in MSI's CFF96.

Good luck,

Pieter Stouten                              ||
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