[Xplor-nih] planeDistPot

[Charles at Schwieters.org]

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Hello Jeff--

> 
>  
> 
> I have used eginput/prot_prot/sa_cross_tor.inp as a starting point for a
> similar calculation that included classic Xplor harmonic plane restraints. I
> would now like to use the new planeDistPot instead of classic Xplor harmonic
> plane restraints. 

Just to be 100% clear: the new term implements
distance-of-atom-to-a-plane restraints. The XPLOR planar restraints term
restrains atoms to lie in the same plane.

>   I expect that to use planeDistPot one has to use the
> python versions of the commands for dynamics and energy minimization or can
> one use the classic Xplor dynamics and energy minimization commands and add
> planeDistPot to a classic include statement? 

One can modifiy old XPLOR scripts to use this new term. Please see below
for details.

>     Can you direct me to any
> examples which use planeDistPot? 

there is a brief example of usage in python/tests/planeDistTest.py

>     I looked at the xplorNIH python reference
> manual but I can't find the format required for specifying the atoms that
> define the plane (oAtom, xAtom, and yAtom). Can you provide a description
> and/or example of the format required for specification of the atoms
> defining the plane? My calculation will include two molecules, one will
> undergo dynamics and energy minimization and the other will be fixed and
> contain the atoms defining the plane.

instead of specifying A,B,C,D (coefficients of plane equation), specify
oAtom,xAtom,yAtom in create_PlaneDistPot. If the line gets too long,
there are other workarounds.

do let me know how it goes.

Charles



using PlaneDistPot in the XPLOR interface

!set up the potential term

eval( $plane_k=1. )

CPYTH "from planeDistTools import create_PlaneDistPot"
! specify plane using equation A x + B y + C z + D = 0
!
CPYTH "c= create_PlaneDistPot"
!this next line can't be longer than 132 characters!
CPYTH "p = c('plane',restraintsFile='plane.tbl',oAtom='name N and resi 15',oAtom='name C and resi 15',oAtom='name O and resi 15')"
CPYTH "planePot=pp"
CPYTH "planePot.setShowAllRestraints(True)"

CPYTH "plane_k = float( xplor.command('','k_plane')[0] )
CPYTH "planePot.setScale(plane_k)"

CPYTH "xplor.simulation.potList().append( planePot )"

flags include SCRIpting end

rest of script....

You may wish to scale the force constant plane_k during cooling- as is
done with normal distance restraints. To set the force constant, you
need two lines, after you set $k_plane appropriately:

CPYTH "plane_k = float( xplor.command('','k_plane')[0] )
CPYTH "planePot.setScale(plane_k)"
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