Re: Rotate two linked proteins against each other and calculate energy profile

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Mar 15 2011 - 16:56:39 CDT

Hi,

Perhaps the colvars
module<http://www.ks.uiuc.edu/Research/namd/2.7/ug/node47.html>would
be of interest to you as well. You could define a dihedral colvar
between the two subunits and obtain the free enrgy profile of the rotation.

Best regards,
Ajasja

On Tue, Mar 15, 2011 at 20:20, Bjoern Olausson <namdlist_at_googlemail.com>wrote:

> Hi NAMD users,
>
> I have a homo dimer which is linked via a short peptide linker. The
> two monomers are supposed to rotate more or less free against each
> other.
>
> I would like to follow the energy profile while one monomer is rotated
> 180 degrees to see if there is on favorite position. Something like
> the energy profile when rotating the dihedral angle of an Ethane
> molecule.
>
> I already have a explicite solvent, all-atom simulation running for this
> system.
>
> Now my qestions:
> a) Would I use FEP for the energy profile (Use coordinates from my
> simulation as start structure and as target structure take coordinates
> from a SMD run where I rotate one monomer by 180 degrees)? I guess
> not. Since I can't tell FEP where to go.
>
> b) Instead of using FEP, is it possible to just run a SMD where I
> rotate (rotConstraints) one monomer by 180 degree and calculate the
> forces from the SMD output (like in the NAMD tutorial "Force Analysis
> for Constant Velocity Pulling"
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node19.html#SECTION00064100000000000000
> )?
>
> c) Is it possible to rotate a molecule using tcl forces instead of SMD?
>
> Thanks for you help.
>
> Cheers,
> Bjoern
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:40 CST