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

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Mar 21 2011 - 03:43:55 CDT

Hi Bjoern,

The analogy with ethane is reasonable. So is the definition of the points. A
little though has to be given about which atoms of the subunit will be
included. If you look at the recommendations for colvar
definitions<http://www.ks.uiuc.edu/Research/namd/2.7/ug/node49.html#SECTION000122310000000000000>
you
will note that a lot of atoms in the atom group may hurt scaling and
performance of NAMD. I do not know how big is each subunit. Perhaps is you
include just the C-alpha atoms...?

By using the adaptive biasing force
calculations<http://www.ks.uiuc.edu/Research/namd/2.7/ug/node50.html#SECTION000123100000000000000>
you
do not have to apply any additional forces. Just include your colvar in the
abf block and you're good to go.

Best regards,
Ajasja

On Sun, Mar 20, 2011 at 17:03, Bjoern Olausson <namdlist_at_googlemail.com>wrote:

> Thanks again for your suggestion Ajasja, I am still planing the setup
> and I finally decided to go with "colvars" and "SMD".
>
> I am mulling over your "colvars" and Dihedral suggestion.
> Since it is the first time I am using "colvars" I am somewhat
> uncertain how I should group the atoms.
>
> My current Idea to define a dihedral would be the following:
> Group 1: Monomer A
> Group 2: First half of the linker
> Group 3: Second half of the linker
> Group 4: Monomer B
>
> Does this make sens to you?
>
> To come back to the Ethan molecule, Group 1 would resemble a Proton on
> C1, Group 2 would be C1 itself, Group 3 would be C2 and Group 4 would
> be a Proton on C2.
>
> Is this analogy correct?
>
> Finally I would apply a force to Monomer A (Group 1) to rotate it
> (maybe I have to constrain Monomer B, but we will see)
>
> Does this sound reasonable?
>
> Thanks a lost for your suggestions,
> Bjoern
>
> On Tue, Mar 15, 2011 at 22:56, Ajasja Ljubetič
> <ajasja.ljubetic_at_gmail.com> wrote:
> > Hi,
> > Perhaps the colvars module 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
> >>
> >
> >
>

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