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/ =
> ---------------------------------------------------------------
>
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Received on Mon Sep 22 2008 - 05:08:11 PDT
