Freezing atoms during molecular mechanics

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Freezing atoms during molecular mechanics

Graham Ball

Hi Folks,

 

A quick question – is there any way to freeze atoms during a minimization or conformation search e.g., obconformer routine? 

I know Avogadro can do it but I couldn’t find if there was a command line flag or something in the mol file that I should set to do this.

 

Regards,

 

Graham Ball

 

++++++++++++++++++++++++++++++++++++++
 Graham E. Ball
 School of Chemistry
 University of New South Wales
 Sydney 2052
 AUSTRALIA


 


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Re: Freezing atoms during molecular mechanics

Tim Vandermeersch
Hi,

On Tue, Jun 8, 2010 at 7:11 PM, Graham Ball <[hidden email]> wrote:
> Hi Folks,
>
>
>
> A quick question – is there any way to freeze atoms during a minimization or
> conformation search e.g., obconformer routine?

Yes, for minimization this is possible. I don't think it is currently
possible for the conformer search routines.

> I know Avogadro can do it but I couldn’t find if there was a command line
> flag or something in the mol file that I should set to do this.

This isn't supported out of the box. Avogadro uses the OBFFConstraint
object for this. Implementing this in C++ or python should be easy
though. If you use pybel, it should only take 10-20 lines and doesn't
require to compile anything. Is this an option for you?

Being able to use the constraints from the command line would be nice
though. The easiest solution I can think of is to create a very simple
syntax to define the constrains in a text file. This file could be
specified with a -const argument to the various molecular mechanics
executables. Do you compile from source? If so, I'll try to add it in
the near future. Suggestions for a syntax are always welcome. The
supported constraints (or restrains) are:

void SetFactor  (double factor)
void AddIgnore (int a)
void AddAtomConstraint (int a)
void AddAtomXConstraint (int a)
void AddAtomYConstraint (int a)
void AddAtomZConstraint (int a)
void AddDistanceConstraint (int a, int b, double length)
void AddAngleConstraint (int a, int b, int c, double angle)
void AddTorsionConstraint (int a, int b, int c, int d, double torsion)

Tim

>
> Regards,
>
>
>
> Graham Ball
>
>
>
> ++++++++++++++++++++++++++++++++++++++
>  Graham E. Ball
>  School of Chemistry
>  University of New South Wales
>  Sydney 2052
>  AUSTRALIA
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

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