[gmx-users] secondary structure element constraining

alex rayevsky rayevsky85 at gmail.com
Tue Jun 12 17:07:39 CEST 2018

Yes, it does... Should I follow this advices
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ?

Phi/Psi lines are like in the sample, with only changed values of atom
indexes and angles, measured with pymol of gromacs tools

ai   aj    ak    al |  type  | label  |   phi          | dphi  kfac  power

   my atom indices  | 1      |    1   | measured value | 0       1      2

dphi (seems to be 0 if I want to immobilize this geometry) and kfa (is
equal to 1 or it means 1000kJmol-1nm-2) as I understood, power label are
not implemented and type has only one value = 1. Am I right??

1. find both phi/psi from the strtucture for each residue

2. add to the top file as You corrected here


and why are freezing of COM pulling cylinder code (to allow some
degree of oscilation) less appropriate methods? or simple genrestr
with 10000 kJ forces ?

Thank You!

On 6/10/18 3:04 AM, alex rayevsky wrote:
>* Dear users!
*>>* Did anybody meet the problem of positional constraints applied to the
*>* secondary structure, namely keeping the 310-helix stable all the time? I've
*>* modelled the substructure - a bundle of alpha helices with a 310 helix
*>* segment (longer, thinner, reactive) on the one of them. And I need to hold
*>* this conformation intact, to study other rearrangements. I'm not sure that
*>* freezing is a good way to nail 3-5 residues in a huge system, maybe it is
*>* somehow robust. At the same time I tried to simulate the helix with
*>* restraints (10000 kJ/A^2 XYZ per each atom of the 310 helix part) and the
*>* helix moved to the low energy state with a transition '310 -> alpha
*>* conformation' without any obstacles. Usually I'm using COM pulling code,
*>* but I don't know how to put some constraint on the backbone of these
*>* several residues (forming triangle instead of the square, while looking
*>* through the helix) without any relation to a surrounding system (without
*>* reference atoms), just like a freezing but more realistic, allowing some
*>* harmonic oscillations. Any suggestions??
>It sounds like you want dihedral restraints on your phi and psi torsions.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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