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Original Post (Thread Starter)
#14686 06/16/2007 6:29 AM
by Chaitanya
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..
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#14687 Jun 16th a 03:54 PM
by rmv
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.
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