Re: [AMBER] a pdb-trajout problems

From: bingbing zhang <zbingbing.ruc.gmail.com>
Date: Sat, 25 Sep 2010 18:54:14 +0800

Thank you very very much! It helps me indeed! I get the pdb file with
protein in the water box in which the water molecules are almost
homogeneous.
    Two other problems are bothering me. (i) In the new pdb file, there are
two big hollow spaces on both sides of the box. How could that happened, is
there any possibility that it could be another protein on the edge of the
box ?
(ii) Due to the problem(i), what should I do for getting a pdb file in which
it contains two or three boxes and proteins.
    Is there any suggestion about the problems?

Best regards

-- 
Zhang Bingbing
On Wed, Sep 22, 2010 at 1:08 PM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> Hello,
>
> Try this:
>
> center origin :1-150
> image origin center familiar
>
> That should work... you might also want to try using the rms function if
> you are going watch the trajectories in something like vmd.
>
> -Trevor
>
> ________________________________________
> From: bingbing zhang [zbingbing.ruc.gmail.com]
> Sent: Tuesday, September 21, 2010 7:44 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] a pdb-trajout problems
>
> Thank you very much for your help!  In my case, the water box is a
> truncated
> octahedron.
>
> I have also tried using the "image center" instead of "image center
> familiar", and the water box turns out to be a rhombohedron with the
> protein
> at the edge. I have attach the picture of one of the pdb files. It's
> amazing. Shouldn't the protein be in the center of box when both "center"
> and "image center" are using?
>
> Is there any kind of cases in which water molecule can distribute
> homogeneous?
> Looking forward to your reply!
>
> Best Regards
> --
> Zhang Bingbing
>
>
>
> On Tue, Sep 21, 2010 at 10:42 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > It looks like your system is using a rectangular box. If this is the
> > case try using "image center" instead of "image center familiar". I'm
> > not 100% sure but I think the 'familiar' keyword is only for truncated
> > octahedral boxes.
> >
> > -Dan
> >
> > On Sun, Sep 19, 2010 at 10:57 AM, bingbing zhang
> > <zbingbing.ruc.gmail.com> wrote:
> > > Dear,
> > >
> > > I am using AMBER9 to equilibrate and run production dynamics on a
> > protein.
> > > Everything seems normal during the equilibration progress, but the PDB
> > files
> > > generated by "trajout" have some problems. I run the MD simulation with
> > > "iwrap=1".
> > >
> > >   Form figure1, the picture of one of these PDB files, it is obvious to
> > > find that the protein is at the edge of the box and some atoms stay
> > outside
> > > the water TIP3P box. It seems like there is a big ball-like thing in
> the
> > > space.
> > >
> > >   So I try adding " center :1-150" and " image center familiar" to the
> > > ptraj file to locate the solute molecule into box. Then I get the
> figure2
> > > and 3, picture of new pdb file. In the new pdb, the water molecules are
> > not
> > > homogeneous. I want to get two or more box show in pdb, but I don't
> know
> > how
> > > to get it.
> > >
> > >   Does someone have any suggestion to overcome the problems?
> > >
> > >   Looking forward to getting your help!
> > >
> > >   Thank you very much in advance!
> > >
> > >
> > > Best Regards
> > >
> > > Zhang Bingbing
> > >
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> > >
> > >
> >
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Received on Sat Sep 25 2010 - 04:00:04 PDT