RE: hbond restraint simulation

From: Vermaas, Joshua (
Date: Fri Jan 25 2019 - 14:09:52 CST

Hi Prabir,

While I'm normally a big advocate for letting the force field figure things out, I'd try to get something reasonable first by any means necessary. If you know that the hexamer has some symmetry, I'd exploit that symmetry. Assuming a monomer that is correctly oriented and everything is 60 degrees apart on the wheel something like the following will get you close to a barrel structure:

set monomer [atomselect top "whatever you need to get a monomer selected"]
$monomer moveby [vecscale -1 [measure center $monomer]]
$monomer moveby [list 20 0 0]; #Adjust as needed. The "20" is basically your barrel radius
$monomer writepdb A.pdb
$monomer move [transaxis z 60]
$monomer writepdb B.pdb
#Continue doing this until you have your 6 monomers arranged how you want.

However, that doesn't actually answer your original question. The problem is that a "hbond" colvar only goes between 0 and 1 (see, since a hbond either exists or it doesn't (with a switching function inbetween). Your targets are all too large, so the colvar isn't doing what you want. Change all your "hbond" definitions to "distance", and I think you are in business.


On 2019-01-25 12:24:26-07:00 wrote:

Dear NAMD user,
I am trying to prepare a barrel-shaped oligomer of a protein starting from a monomer. I had
already such a barrel-shaped tetramer structure that I am using as template. Now I am using this tetramer and a dimer from this tetramer placed sufficiantly at optimal distance after avoiding the bad contacts to prepare the hexamer. Only restriction that I need to form such a hexamer is hydrogen bonds between a set of atoms. I am using 54 hbond restraints of which 44 hbonds are already preformed and 10 hbonds are to be formed by the simulation. I am wondering how to decide the force constant to speed up the simulation to achieve the target structure. Please note that I do not need a smooth free energy profile for this as I am interested to prepare the hexamer only that will be used in the final simulation. Here, I am attaching the colvar config file that I am using for the simulation. It seems that the molecules are not moving at all which is likely due to the bad choice of force constant. I am using the initial centers values for this case is the distance between donor and acceptor atom. Can anyone please suggest me an idea how to choose the force constant for my purpose or what parameters to be tuned to speed up this process? Please also point out if I am doing anything wrong in preparing the colvar config file.
Thanking you,

Prabir Khatua
Postdoctoral Research Associate
Department of Chemistry & Biochemistry
University of Oklahoma
Norman, Oklahoma 73019
U. S. A.

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:27 CST