AMBER Archive (2009)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Fri Oct 30 2009 - 00:43:22 CDT

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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>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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