From: Nadia Elghobashi-Meinhardt (nelgho_at_gmail.com)
Date: Fri Oct 02 2020 - 03:54:52 CDT
Many thanks for the suggestion to use SMD, but I
still believe TMD is better suited as
I know exactly the starting coordinates and
end coordinates for the ligand. I am interested in
the transition path connecting these two ligand positions.
Perhaps someone can advise regarding "fitting" and "biasing"
atom selections? Should I be using one domain or two domains?
On Thu, Oct 1, 2020 at 4:14 PM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
> Dear researcher,
> TMD is not suitable for ligand binding problems.
> Use steered molecular dynamics (SMD).
> TMD is specialized to extract conformational transition pathways
> and the associated hot sites involved in the transition.
> *All the best,*
> *Ashkan Shekaari,*
> *Ph.D Candidate in Solid State Physics,*
> *K. N. Toosi University of Technology,*
> *Tehran, Iran*
> *From: *"Nadia Elghobashi-Meinhardt" <nelgho_at_gmail.com>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>
> *Sent: *Thursday, October 1, 2020 5:29:18 PM
> *Subject: *namd-l: TMD questions - refined
> Dear NAMD experts,
> I am refining the questions I posted recently in the
> hope that a TMD expert out there will respond with
> some guidance.
> I am trying to use TMD to steer a ligand (28 atoms) in a protein (1260
> atoms) -
> equilibrated system - to a binding pocket that is 15Angstrom away from the
> ligand's initial position. Are the following setup steps reasonable?
> 1) Only protein Calpha atoms and ligand heavy atoms in target position are
> in target.pdb
> 2) The protein is assigned to domain 1 and ligand to domain 2 in
> the beta column
> 3) The *protein is fitted but not biased in domain1*
> 4) The *ligand is fitted and biased in domain2*
> 5) TMDk is 200 in the configuration file
> The problem I am having is the following:
> over the course of 5ns simulation, barely
> any movement of ligand in the direction of target coordinates is observed.
> A more general question: Is TMD appropriate for the investigation of
> ligand binding or would a colvar_rmsd approach be more suitable?
> Any suggestions or tips are a great help!
> Thank you in advance.
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