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Posted By: Chaitanya helix backbone constraints - 06/16/07 06:29 AM
Hi everyone,

I want to energy minimise an alpha helix using harmonic constraints on the backbone atoms and fixing the psi and phi dihedrals to their standard values

CONS HARM sele (selection for backbone atoms) end
CONS DIHE (dihedral specifications)

followed by energy minimization. Will this do??could someone please suggest how it should be done..
Posted By: rmv Re: helix backbone constraints - 06/16/07 03:54 PM
CONS DIHE used to be the only choice, and required a loop over the helix residues, e.g. for residues 22-45 of segment A--

set k 22 ! FIRST RES
label rhlx
calc m = @K + 1
cons dihe A @K N A @K CA A @K C A @M N force 100. min -47 ! psi
cons dihe A @K C A @M N A @M CA A @M C force 100. min -57 ! phi
incr k by 1
if k lt 44 goto rhlx

However, a few years ago CONS HARM was enhanced with a couple new keywords, notably the BESTFIT option--

cons harm bestfit mass force 1. sele resid 22:45 .and. -
( type N .or. type CA .or. type C ) end

The force values differ so much because the CONS DIHE force units are force/radian, while the CONS HARM units are (mass weighted) force/A^2. Note that CONS HARM without a 3rd keyword reverts to CONS HARM ABSOlute, which restrains the atom coordinates; the BESTFIT option restrains the RMS coord difference after alignment via rotation and translation, and thus restrains the shape of the group of selected atoms.
Posted By: Chaitanya Re: helix backbone constraints - 06/17/07 05:50 AM
Hi rmv,

Thanks a lot. I used the first option initially (the loop), but the CONS HARM BESTFIT looks simple. I have a small doubt. I would also like to apply the harmonic constraints on the backbone atoms(absolute)in addition to constraining the dihedrals . So should I use the CONS HARM option on all the back bone atoms or will the CONS HARM BESTFIT option takes care of it?
Posted By: rmv Re: helix backbone constraints - 06/17/07 02:43 PM
Try not to overuse restraints; just use the fewest needed for a short term goal. Use only one of CONS DIHE, CONS HARM BESTFIT, or CONS HARM ABSOLUTE. The absolute restraints are generally the least useful. Which ones you use depends on the molecule and the goal.

These kinds of restraints are appropriate for model building and minimization, but usually are not appropriate for simulations.
Posted By: Chaitanya Re: helix backbone constraints - 06/18/07 06:05 AM
Hello rmv,

Thanks a lot for the advice.
Posted By: hkhandel Re: helix backbone constraints - 06/18/07 08:37 AM
In continuation to the above discussion, does this mean that one can drive a random coil peptide into helical form using the constraint and best-fit commands discussed above ? Or does one need to have coordinates of the helical form a-priori as comparison coordinates ?
Posted By: Chaitanya Re: helix backbone constraints - 06/18/07 02:00 PM
One need not have the coordinates of a helix as a reference. You can convert any random coiled protein to helix by setting the dihedral values to standard values (phi -57 & psi -47)or close to them using the 'ic edit' command. These constraints are used to maintain the helical conformation during energy minimization or dynamics (otherwise it may revert back to random coil conformation)
Posted By: rmv Re: helix backbone constraints - 06/18/07 04:02 PM
Using CONS DIHE alone may be enough to drive a random fold to a helix, possibly with gradually increasing force constants.

The CONS HARM options (ABSOlute, BESTfit, RELAtive) require some coords in a helix, but they need not be the coords for the restrained residues, as long as the number of atoms is the same and there is a direct correspondence between each atom in the restraint set and the reference set. This can be done directly with the RELAtive option; the other options require a couple extra steps--

COOR COPY COMP
COOR DUPL SELE reference-atoms END SELE restraint-atoms END COMP
CONS HARM BEST SELE restraint-atoms END COMP ...

You may also wish to explore the use of CONS RMSD
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