On 6/7/13 8:43 PM, Sanku M wrote:
Hi,
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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