[BiO BB] Molecular Mechanics (Universal Force Fields models)

Peter Oledzki biopolak at yahoo.co.uk
Mon Nov 3 08:57:44 EST 2003


quoting you val "it does not help much in answering
real questions in (bio)chemistry and bioinformatics"
I would have to disagree these sort of calculations
are used in structure based drug design all the time.
The big pharma companies are using these sort of
calculations to screen for lead componds and the
preliminary results for current methods are


 --- val <val at vtek.com> wrote: > Hi Miguel,
>     Google is your best friend.  Try, e.g., google
> with
> 'molecule energy software'.
>     But i wouldn't rely much on this type of
> calculation; it does not help much in answering real
> questions in (bio)chemistry and bioinformatics.
> my best,
> val
> ----- Original Message -----
> From: Miguel Pignatelli
> To: bio_bulletin_board at bioinformatics.org
> Sent: Thursday, October 30, 2003 4:43 AM
> Subject: [BiO BB] Molecular Mechanics (Universal
> Force Fields models)
> Hi,
> I'm trying to make a program in C that calculates
> the energy of a molecule
> from the coordinates X,Y,Z of its atoms. We want to
> apply the Universal
> Force Fields (UFF) described by Rappe. Once we have
> the total energy of the
> molecule (contribution from each chemical bond (bond
> stretching), angle
> bending, torsional terms, improper torsions, out of
> plane bending motions
> and non-bonded interactions (electrostatic and Van
> der Waals forces)) we
> will look for energy minimisation through the
> conjugate gradient
> minimisation method.
> I am looking for a similar software to look at or
> any algorithm that could
> help me. First of all I would like to know what is
> the best data structure
> to use in this kind of software and if there is any
> similar software to look
> at its code or any algorithm that implements the
> UFF.
> The software imput will be atoms and coordinates, so
> it will determine which
> atoms are bonded. Is there any efficient algorithm
> for that?
> Any suggestions?
> Thanks all
> _______________________________________________
> BiO_Bulletin_Board maillist  - 
> BiO_Bulletin_Board at bioinformatics.org

Peter Oledzki
Department of Biochemistry and Molecular Biology
University of Leeds,UK

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