AW: PBC in lipid bilayer: receptor vs. ligand

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jan 27 2016 - 09:35:05 CST

Hi,

generally I wouldn't recommend to use NAMDs wrapping stuff and better do it afterwards from within VMD, as you have better control on it.

For now, you could try the following in VMD:

1. Repair overlong bonds due the wrapping by doing:
     pbc join connected
2. Wrap again by centering around your binding site:
     pbc wrap -all -compound res -center com -centersel "your binding site selection text"

Norman Geist

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von R. Charbel MAROUN
> Gesendet: Mittwoch, 27. Januar 2016 14:55
> An: Namd Mailing List <namd-l_at_ks.uiuc.edu>
> Betreff: namd-l: PBC in lipid bilayer: receptor vs. ligand
>
> 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.i
> np
>
> 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.
>
> # You have some freedom choosing the cutoff
> cutoff 12.0; # may use smaller, maybe 10.,
> with PME
> switchdist 10.0; # cutoff - 2.
> # switchdist - where you start to
> switch
> # cutoff - where you stop
> accounting for nonbond interactions.
> # correspondence in charmm:
> # (cutnb,ctofnb,ctonnb =
> pairlistdist,cutoff,switchdist)
> pairlistdist 14.0; # stores the all the pairs with
> in the distance it should be larger
> # than cutoff( + 2.)
> stepspercycle 20; # 20 redo pairlists every ten
> steps
> pairlistsPerCycle 2; # 2 is the default
> # cycle represents the number of
> steps between atom reassignments
> # this means every 20/2=10 steps
> the pairlist will be updated
>
> # Integrator Parameters
> timestep 2.0; # fs/step
> rigidBonds all; # Bound constraint all bonds
> involving H are fixed in length
> nonbondedFreq 1; # nonbonded forces every step
> fullElectFrequency 1; # PME every step
>
> wrapWater on; # wrap water to central cell
> wrapAll on; # wrap other molecules too
> wrapNearest off; # use for non-rectangular cells
> (wrap to the nearest image)
>
> # PME (for full-system periodic electrostatics)
> source checkfft.str
> margin 2.5;
> PME yes;
> PMEInterpOrder 6; # interpolation order (spline
> order 6 in charmm)
> PMEGridSizeX $fftx; # should be close to the cell
> size
> PMEGridSizeY $ffty; # corresponds to the charmm input
> fftx/y/z
> PMEGridSizeZ $fftz;
>
> # Constant Temperature Control
> set temp 323.15;
> langevin on; # langevin dynamics
> langevinDamping 1.0; # damping coefficient of 1/ps
> (keep low)
> langevinTemp $temp; # random noise at this level
> langevinHydrogen no; # don't couple bath to hydrogens
> reinitvels $temp;
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes; # use a hydrogen-group based
> pseudo-molecular viral to calcualte pressure and
> # has less fluctuation, is needed
> for rigid bonds (rigidBonds/SHAKE)
> useFlexibleCell yes; # yes for anisotropic system like
> membrane
> useConstantRatio yes; # keeps the ratio of the unit
> cell in the x-y plane constant A=B
>
> langevinPiston on; # Nose-Hoover Langevin piston
> pressure control
> langevinPistonTarget 1.0; # target pressure in bar 1atm =
> 1.01325bar
> langevinPistonPeriod 50.0; # oscillation period in fs.
> correspond to pgamma T=50fs=0.05ps
> # f=1/T=20.0(pgamma)
> langevinPistonDecay 25.0; # oscillation decay time. smaller
> value correspons to larger random
> # forces and increased coupling
> to the Langevin temp bath.
> # Equall or smaller than piston
> period
> langevinPistonTemp $temp; # coupled to heat bath
> run 1500000; # 3ns
>
>
>
> --
> R. Charbel MAROUN, Ph.D., H.D.R.
> UMR-S INSERM U1204/UEVE
> Structure et activité des biomolécules
> normales et pathologiques
> Université d'Evry-Val d'Essonne
> Bâtiment Maupertuis
> Rue du Père Jarlan
> 91000 EVRY
> FRANCE
> Tél: +33 1 69 47 76 64
> FAX: +33 1 69 47 02 19
> e-mail charbel.maroun_at_inserm.fr

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