The picture is not so clear. I do not know what you are looking for in
your simulation, but if the residue numbers 1 to 96 describe the whole
protein, and if 'image familiar com :1-96' created this re-imaged
cell box, then that is how your structure looks like in the simulation.
On Sun, 21 Sep 2008, Qiuting Hong wrote:
> Dear Llyas,
>
> Yes, the reimaged trajectory is different from the one I got before, but
> part of the side chain is still outside the water box. I attach
> a picture. Do you think I failed in this simulation?
> Thank you.
>
> Qiuting Hong
>
> On Sun, Sep 21, 2008 at 1:45 PM, Ilyas Yildirim
> <yildirim.pas.rochester.edu>wrote:
>
> > Qiuting, try the following:
> >
> > -------- ptraj_reimage.in-----------
> > ptraj 1wgg.prmtop << EOF
> > trajin 1wggmd1.mdcrd
> > trajin 1wggmd2.mdcrd
> > trajin 1wggmd3.mdcrd
> > trajout 1wgg_md_reimaged.mdcrd
> > image familiar com :1-96
> > go
> > ------- ptraj.reimage.in---------
> >
> >
> > On Sun, 21 Sep 2008, Qiuting Hong wrote:
> >
> > > Dear Llyas,
> > >
> > > Thank you for your response. Below is my ptraj file:
> > > -------- ptraj_reimage.in-----------
> > > ptraj 1wgg.prmtop << EOF
> > > trajin 1wggmd1.mdcrd
> > > trajin 1wggmd2.mdcrd
> > > trajin 1wggmd3.mdcrd
> > > trajout 1wgg_md_reimaged.mdcrd
> > > center :1-96
> > > image familiar
> > > go
> > > EOF
> > > ------- ptraj.reimage.in---------
> > >
> > > Is this what you mean? But when I check the movie of
> > 1wgg_md_reimaged.mdcrd,
> > > the tip of the side chain dip into the vacuum. I want to know if I need
> > to
> > > re-run the simulation.
> > >
> > > Qiuting Hong
> > >
> > >
> > > On Fri, Sep 19, 2008 at 5:00 PM, Ilyas Yildirim
> > > <yildirim.pas.rochester.edu>wrote:
> > >
> > > > Can you try the following in the ptraj imaging?
> > > > --------- ptraj_imaging.in ------------
> > > > .(your trajin files)
> > > > .(your trajin files)
> > > > .(your trajin files)
> > > > image familiar com :(the first res of the protein)-(last res. of the
> > > > protein)
> > > > ---------------------------------------
> > > > What this will make is to make sure that the center-of-mass of the
> > protein
> > > > will be at the origin. Hope this helps.
> > > >
> > > > PS: I assume that you did not change the box info in the prmtop file.
> > > >
> > > > > I am doing MD for a mouse ubiquitin, 1wgg, which has a long side
> > chain.
> > > > When
> > > > > I solvate the protein, I try solvateoct TIP3PBOX 12.0 and
> > > > > solvateoct TIP3PBOX 10.0. And I find out that the size of solute vdw
> > > > > bounding box is same: 36.162, 30.853, 52.074. So, I decide to use
> > > > TIP3PBOX
> > > > > 10.0 since it has less water molecules.
> > > > >
> > > > > In the amber tutorial, it asks us to reimage all the water molecules
> > into
> > > > > the original box. So I did it, and I find out that a very small part
> > of
> > > > my
> > > > > protein side chain drift into the vacuum after 1ns.
> > > > >
> > > > > However, if I don't reimage the water molecules into the original
> > box,
> > > > the
> > > > > whole protein is still in water. I am wondering whether or not my
> > protein
> > > > > drifts out of water box. Do I trust the reimaged trajectory or the
> > > > original
> > > > > trajectory?
> > > > >
> > > > > If my protein do drift out ot the water box, how do I fix it? I think
> > I
> > > > need
> > > > > to enlarge the water box, but both TIP3PBOX 12.0 and TIP3PBOX 10.0
> > give
> > > > me
> > > > > the same size of water box. I know that if I don't truncate the
> > waterbox,
> > > > I
> > > > > won't have this problem. But I don't want to use so many water
> > molecule
> > > > in
> > > > > the simulation.
> > > >
> > > > --
> > > > Ilyas Yildirim, Ph.D.
> > > > ---------------------------------------------------------------
> > > > = Hutchison Hall B#10 - Department of Chemistry =
> > > > = - University of Rochester =
> > > > = 585-275-6766 (office) - =
> > > > = http://www.pas.rochester.edu/~yildirim/ =
> > > > ---------------------------------------------------------------
> > > >
> > > > -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber.scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> > > > to majordomo.scripps.edu
> > > >
> > >
> >
> > --
> > Ilyas Yildirim, Ph.D.
> > ---------------------------------------------------------------
> > = Hutchison Hall B#10 - Department of Chemistry =
> > = - University of Rochester =
> > = 585-275-6766 (office) - =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> > to majordomo.scripps.edu
> >
>
--
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
= http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Mon Sep 22 2008 - 05:09:17 PDT
