[gmx-users] secondary structure element constraining

[alex rayevsky]

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

https://www.researchgate.net/post/How_can_I_change_and_fix_dihedral_angle_during_Gromacs_simulation_using_dihedral_restraints


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

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
(540) 231-3129http://www.thelemkullab.com