Subject: Re: CCL:Re Charmm - alpha carbons constraint

From: [email-masked] (Don Gregory)
Date: Sun, 17 Dec 1995 13:00:04 -0500

On Dec 16th, A J Turner wrote: 
> I want to prevent Charmm from trying to change 
>the bulk structure of the enzyme - just the small scale structure.
>
>Does anyone have experiance of this - what sort of constraint would be 
>best - and maybe if there is an easy way on defining the selection.
>
A J, I would recommend using a harmonic restraint to hold the
alpha-carbons *close* to their current positions, but allowing them
some flexibility.
Of course, the easy thing to do, is to *fix* the atoms in space, this
can be done with:
CONS FIX SELE TYPE CA END
Assuming, of course, all the alpha carbons are named CA.

Restraining with the harmonic potential is just as easy, as long
as one knows the force constant to apply.  

CONS HARM SELE TYPE CA END FORCE 100.0 

Determining the force constant depends on what forces (energy)
you want to counter-balance with the restraint.  For example,
if you want to make sure the restraint can counter any opposing
bond stretching, you might want to apply a counter restraint
such that if the alpha carbon moves 1 Angstrom away from its
current position, it would impose a restraint of 100 kcal/mol,
analogous to bond stretching.
To do this, simply apply a force constant of 100.
This is what I've done in the above example; a complete description
of these CHARMm commands can be found in the "data/doc" directory
if you have an installation of Quanta. 
Alternatively, you can see these commands via the web, looking at
the support pages of "http://www.msi.com".

Don Gregory