AMBER Archive (2009)

Subject: Re: [AMBER] [Fwd: ligand exiting a protein cavity]

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Oct 29 2009 - 10:17:40 CDT

Hello,

This artifact does occur in many simulations, as long as ntb=1 or ntb=2
(i.e. if you have periodic boundary conditions for constant volume or
constant pressure simulations, respectively). It is purely a visualization
effect, though, since in the simulation every periodic box is included in
the calculation (thus, even if the ligand appears to jump to the other side
of the box, there is still one inside the protein from a different box in
the simulation). Moreover, I believe that this is a side-effect of setting
iwrap=1. iwrap maps molecules that exit the box over to the other side
(since when a molecule exits on one side it must enter on the other in the
periodic box). However, if you don't turn iwrap on (i.e. iwrap=0), then you
will see the effect of the water box 'exploding' as waters diffuse into
neighboring boxes (so the end result is the visualized waters reside in
several different *adjacent* boxes).

However, when you say 'exits', that is unclear. If the situation described
above is what is actually happening to your system, then you should see the
protein approaching the edge of the water box, and the ligand abruptly
jumping 10s of angstroms away from the protein (depending, of course, on the
size of your box). However, if it's a diffusion process where the ligand
slowly migrates out of the cavity as part of your simulation, then that's
not really anything that has gone wrong with the simulation -- it has simply
diffused out. You should be able to tell the difference between these two
occurences simply by visualizing your trajectory.

Good luck!
Jason

On Thu, Oct 29, 2009 at 10:44 AM, Kshatresh Dutta Dubey <kshatresh_at_gmail.com
> wrote:

> I had faced same problem during the simulation of a protein ligand complex,
> when i run the simulation, after 1ns simulation the ligand jumped out of
> cavity. I am not sure, but this problem occurs due to the image of the
> atom/molecules during simulation, which does not effect quality of
> simulation. Simulations in this state are quite well. We may proceed it.
> I am also seeking for others reply so that i can confirm myself.
>
> Kshatresh
>
> On Thu, Oct 29, 2009 at 6:06 PM, <moitrayee_at_mbu.iisc.ernet.in> wrote:
>
> > Some more information along with the problem pasted below.
> > I should also mention that the ligand is held by a loop that moves
> outward
> > when
> > the ligand departs. Actually this loop in my protein has two states, open
> > (in
> > the native form) and closed (in the ligand bound form). In the ligand
> bound
> > form, after some time the loop moves out to exit the ligand.
> > Please suggest me what to do.
> > Thanks a lot.
> >
> > Sincere Regards,
> > Moitrayee
> >
> > ------------------------------- Original Message
> > -------------------------------
> > Subject: ligand exiting a protein cavity
> > From: moitrayee_at_mbu.iisc.ernet.in
> > Date: Thu, October 29, 2009 5:57 pm
> > To: "AMBER Mailing List" <amber_at_ambermd.org>
> >
> >
> --------------------------------------------------------------------------------
> >
> > Dear Amber Users,
> >
> > I am facing a weird problem with my protein.
> > The protein has a high resolution crystal structure (2.1 ang.) and is
> used
> > for
> > my simulation. It is bound with a ligand for which I derived the
> parameters
> > using Gaussian 03 and antechamber module of AMBER. I do minimizations and
> > equillibrations before starting the production run. There is no error as
> > such.
> > However towards the end of the production run at room temp. the ligands
> > exits
> > the protein cavity.
> > My md.in file is as follows:
> >
> > &cntrl
> > imin=0,
> > ntx=7, irest=1,
> > ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
> > ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
> > cut=10.0,
> > nscm=50,
> > nstlim=5000, dt=0.002,
> > tempi=300., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
> > ntp=1, taup=0.5,
> > ntc=2, tol=0.00001,
> > &end
> > &ewald
> > vdwmeth=1,
> > &end
> >
> > What can be the possible problems ?
> >
> > Thanks a lot in advance.
> >
> > Sincere Regards,
> > Moitrayee
> >
> >
> >
> > --
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> >
> >
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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