Try to center first the receptor, image everything back to that, then center
the whole complex and reimage again. i.e.
center :1-371 mass origin
image origin center bymask familiar
center :1-372 mass origin
image origin center bymask familiar
Where I am simulating a protein with ligand, and residues 1-371 belong to
the receptor and the last residue, 372, is the ligand. Adjust accordingly
for your system. This script has, in the past, properly recentered and
imaged my trajectories.
Good luck!
Jason
On Fri, Oct 30, 2009 at 9:42 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> 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.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.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.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.mbu.iisc.ernet.in
> >> >> > Date: Thu, October 29, 2009 5:57 pm
> >> >> > To: "AMBER Mailing List" <amber.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
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > This message has been scanned for viruses and
> >> >> > dangerous content by MailScanner, and is
> >> >> > believed to be clean.
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > ---------------------------------------
> >> > Jason M. Swails
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Graduate Student
> >> > 352-392-4032
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > --
> >> > This message has been scanned for viruses and
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> >> >
> >> >
> >> --
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> >> dangerous content by MailScanner, and is
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> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > ---------------------------------------
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > This message has been scanned for viruses and
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> >
> >
>
>
>
>
>
> --
> This message has been scanned for viruses and
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> believed to be clean.
>
>
> _______________________________________________
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 30 2009 - 09:30:04 PDT
