Re: PBC in lipid bilayer: receptor vs. ligand

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jan 27 2016 - 09:21:11 CST

Hi!

Using PBCTools <http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/> you
should be able to unwrap your trajectory.

Best,
Ajasja

On 27 January 2016 at 14:54, R. Charbel MAROUN <charbel.maroun_at_inserm.fr>
wrote:

> Hello NAMD users:
>
> I have a receptor embedded in a lipid bilayer. The receptor has a ligand
> in its binding site. After several hundred ps of MD, the receptor (and the
> ligand) move away from the center of the membrane in the plane of the
> membrane. As I have applied PBC, when the receptor gets away far enough
> from the membrane, its image appears at the other side. Sometimes, it's the
> image of the ligand that appears in the other side. This depends on whether
> the receptor or the ligand attains the border of the cell. As a
> consequence, the receptor and ligand get unpaired for many frames, ie, the
> ligand is not in the binding site. Apparently, the ligand continues to
> behave as if in it. The problem comes if I want to measure, for ex.,
> distances between ligand and residues for those frames, or make statistics
> out of my trajectory. Below is the inp file I'm using.
>
> Is there any way around, such as imposing a constraint to the ligand, so
> that it follows the receptor, even if the ligand doesn't "hit" the border
> of the cell ?
>
>
>
> structure C_3CAP-H2ODow-HME_sol_ion.psf
> coordinates C_3CAP-H2ODow-HME_sol_ion.pdb
>
> outputName step74_prod; # base name for output from this run
> # NAMD writes two files at the end,
> final coord and vel
> # in the format of first-dyn.coor
> and first-dyn.vel
>
> set inputname step73_prod;
> binCoordinates $inputname.restart.coor; # coordinates from last run
> (binary)
> binVelocities $inputname.restart.vel; # velocities from last run
> (binary)
> extendedSystem $inputname.restart.xsc; # cell dimensions from last
> run (binary)
>
> firsttimestep 2254880; # last step of previous run
> restartfreq 500; # 500 steps = every 1ps
> dcdfreq 1000;
> dcdUnitCell yes; # the file will contain unit cell
> info in the style of
> # charmm dcd files. if yes, the dcd
> files will contain
> # unit cell information in the
> style of charmm DCD files.
> xstFreq 500; # XSTFreq: control how often the
> extended systen configuration
> # will be appended to the XST file
> outputEnergies 125; # 125 steps = every 0.25ps
> # The number of timesteps between
> each energy output of NAMD
> outputTiming 500; # The number of timesteps between
> each timing output shows
> # time per step and time to
> completion
>
> # Force-Field Parameters
> paraTypeCharmm on; # We're using charmm type parameter
> file(s)
> # multiple definitions may be used
> but only one file per definition
>
> # parameters
> /usr/local/vmd-.9/lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
>
> parameters
> /home/cmaroun/toppar/toppar_27/par_all27_prot_lipid_cholesterol_HME_TIP3.prm
> parameters /home/cmaroun/readcharmmpar1.2/par_all36_lipid.prm
>
> # These are specified by CHARMM
> exclude scaled1-4 # non-bonded exclusion policy to
> use "none,1-2,1-3,1-4,or scaled1-4"
> # 1-2: all atoms pairs that are
> bonded are going to be ignored
> # 1-3: 3 consecutively bonded are
> excluded
> # scaled1-4: include all the 1-3,
> and modified 1-4 interactions
> # electrostatic scaled by
> 1-4scaling factor 1.0
> # vdW special 1-4 parameters in
> charmm parameter file.
> 1-4scaling 1.0
> switching on
> vdwForceSwitching yes; # New option for force-based
> switching of vdW
> # if both switching and
> vdwForceSwitching are on CHARMM force
> # switching is used for vdW forces--001a1136812827aa17052a525a50--

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