[gmx-users] maining helix conformation
jalemkul at vt.edu
Sat Jun 8 02:54:05 CEST 2013
On 6/7/13 8:43 PM, Sanku M wrote:
> I have a pair of polypeptides which are generated as ideal helix. I want to carry out their assembly/dis-assembly simulation by maintaining the helicity of them.
> I wonder which of the methods for retaining helicity is better :
> 1. use a harmonic restraints using [bonds] directive using type 6 among the backbone amide Hbond between i and i+4th residue.
> 2. Use dihedral restraint to maintain phi and Psi.
> Any help will be appreciated.
Either should work. Method 2 may be slightly more direct and less error-prone
since the restraints can be easily written using genrestr.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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