AMBER Archive (2009)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Fri Oct 30 2009 - 08:42:57 CDT

I had used the following ptraj action commands during the crd to pdb extraction:

 rms first out rms @CA
 center @CA
 image
 strip :WAT
 go

But I got the mentioned problem. It would be of immense help to me if you please
comment/suggest on this.

Best Regards,
Moitrayee

It does sound like the artifact previously described. Ptraj has the ability to
recenter and reimage everything in the same box. See the center and image
commands in the ambertools manual for ptraj.
>
> Good luck!
> Jason
>
> On Fri, Oct 30, 2009 at 1:43 AM, <moitrayee_at_mbu.iisc.ernet.in> wrote:
>
>> Thanks a lot for your reply. When I see my whole trajectory in VMD, the ligand
>> is placed in the protein cavity and does not diffuse out. However, when I pick
>> up a snapshot and try to visualize one single pdb the ligand is placed out the
>> protein at a certain distance in some cases.
>> I have ntb=2 and iwrap = 1.
>> I think it is just a visualization effect as you had mentioned. Thanks once
again.
>> Sincere Regards,
>> Moitrayee
>> > 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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>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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