From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Dec 13 2018 - 09:39:28 CST
Please keep the conversation on-list.
There are several possible ways to go about this. One way is to fix some
atoms, I suppose, but better use NAMD "constraints", which are actually
restraints. A misnomer that I hope will be corrected eventually.
Another way is to use the Colvars Module to apply a force on an internal
coordinate of the protein-ligand system.
On Thu, 13 Dec 2018 at 16:18, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
> Interesting, so it is not required to fix any atoms? The force, if set up
> correctly, should only pull on the ligand and the rest of the system should
> behave normally? I use constantforce yes, and consforcefile myfile.ref, and
> within myfile.ref only the atoms for the ligand have a value in the
> occupancy column, the others are zeroes, and the x y z of the ligand atoms
> are set to 0.00 0.00 1.00, so that they are pulled in the positive z
> direction, the other atoms' coordinates were left unchanged.
> Kelly L. McGuire
> PhD Candidate
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602
> *From:* Jérôme Hénin <jerome.henin_at_ibpc.fr>
> *Sent:* Thursday, December 13, 2018 6:06:12 AM
> *To:* Namd Mailing List; McGuire, Kelly
> *Subject:* Re: namd-l: Constant Force Pull
> My advice would be to just pull on the ligand with a counter-force on some
> protein atoms, distributed around the binding site. There should be no need
> for any restraint on the membrane, that's a symptom that something else is
> very wrong.
> On Thu, 13 Dec 2018 at 10:48, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
> I am trying to do a constant force pull on my ligand, pulling it out of
> a protein. I have the backbone atoms and certain atoms in the DMPC
> membrane constrained. The force on the ligand is 1 kcal/mol/A^2 or 69.479
> pN A. As the ligand is moving, the waters on both sides of the membrane
> expand away from the membrane the simulation stops with the error:
> ERROR: Constraint failure in RATTLE algorithm for atom 60956!
> ERROR: Constraint failure; simulation has become unstable.
> Before I put a constraint on the membrane, it was separating in opposite
> directions along the z-coordinate. As for the water, I can't constrain
> those or the simulation stops with periodic boundary errors. How do I do a
> constant force pull on a ligand in a protein/membrane/water system?
> *Kelly L. McGuire*
> *PhD Candidate*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*
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