Dear Joung,
Thank you very much for your explanation.
Best,
Xioling
> Date: Tue, 3 Aug 2010 14:04:32 -0400
> From: i.joung.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] PTRAJ: problem with image command
>
> Ptraj 'distance' command does image implicitly, so it will always give you
> the shortest distance between the two groups unless 'noimage' is specified.
> If what you want is the *shortest* distance, you should not put 'noimage'.
>
> I don't know about Rasmol, but I am pretty sure that distance command of
> ptraj will not work differently from other software.
> 'properly coordinated' is really dependent on the properties you want to
> investigate. Imaging can be done enormous ways and there is no universally
> good imaging.
>
> You wrapped molecules but
>
>
> On Tue, Aug 3, 2010 at 12:17 PM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> >
> > Dear Joung,
> >
> > Thanks alot for your answer. Anyway, to calculate the distance between ions
> > and residue 1, do we need to set residue 1 as the center (i.e. without
> > 'noimage') ?
> >
> > I think that at the first step which we already shifted molecules back into
> > the primary unit cell (with command 'image origin center' and centered on
> > DNA) we should get properly coordinates of all Na+/WAT. And then we can
> > directly calculate distance between 2 molecules (e.g. distance between WAT
> > and Na+). In other words, we can measure distance between 2 atoms using
> > Rasmol after we extracted snapshots as PDB file. Or even we can perform
> > further calculation (e.g. interaction between any molecules). Am I right?
> >
> >
> >
> > Xioling
> >
> >
> >
> > > Date: Tue, 3 Aug 2010 11:20:13 -0400
> > > From: i.joung.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] PTRAJ: problem with image command
> > >
> > > Hi,
> > > You imaged with respect to your whole solute(:1-20) not the residue
> > 1(:1).
> > > This means that residue 1 is not always in the center. In this case, if
> > you
> > > specify 'noimage', some of the distances between a solvent molecule and
> > > residue 1 can be farther than the distances calculated without 'noimage'.
> > >
> > > On Tue, Aug 3, 2010 at 10:30 AM, Xioling Chuang <xioling_c.hotmail.com
> > >wrote:
> > >
> > > >
> > > > Dear All,
> > > >
> > > >
> > > >
> > > > I am using amber9 and tried to perform MD simulation of polyAT 10-mer.
> > > > After MD simulation, I used ptraj to shift molecules back into the
> > primary
> > > > unit cell using the following script
> > > >
> > > > ----------------------->
> > > >
> > > > trajin polyAT.mdcrd
> > > >
> > > > trajout polyAT.trj
> > > >
> > > > center :1-10 mass origin
> > > >
> > > > image origin center
> > > >
> > > > center :1-20 mass origin
> > > >
> > > > image origin center
> > > >
> > > > go
> > > >
> > > > <-----------------------
> > > >
> > > >
> > > >
> > > > Then I tried to calculate the distance between Na+ ions and some
> > residue,
> > > > e.g. residue#1, using two different script files (with/wothout option
> > > > noimage), as below;
> > > >
> > > >
> > > >
> > > > "dist1.in"
> > > >
> > > > ------------------------------>
> > > >
> > > > trajin polyAT.trj
> > > >
> > > > distance jj1 :21 :1 out dist1.Na1.dat
> > > >
> > > > distance jj2 :22 :1 out dist1.Na2.dat
> > > >
> > > > distance jj3 :23 :1 out dist1.Na3.dat
> > > >
> > > > distance jj4 :24 :1 out dist1.Na4.dat
> > > >
> > > > go
> > > >
> > > > <-----------------------------
> > > >
> > > >
> > > >
> > > > "dist2.in"
> > > >
> > > > ------------------------------>
> > > >
> > > > trajin polyAT.trj
> > > >
> > > > distance jj1 :21 :1 out dist2.Na1.dat noimage
> > > >
> > > > distance jj2 :22 :1 out dist2.Na2.dat noimage
> > > >
> > > > distance jj3 :23 :1 out dist2.Na3.dat noimage
> > > >
> > > > distance jj4 :24 :1 out dist2.Na4.dat noimage
> > > >
> > > > go
> > > >
> > > > <------------------------------
> > > >
> > > >
> > > >
> > > > I expected that I should obtained the same results, since the
> > trajectory
> > > > file "polyAT.trj" was already imaged. However, the obtained results
> > were
> > > > that some outputs are the same, e.g. the distances of all snapshots in
> > > > "dist1.Na1.dat" & "dist2.Na1.dat", but some are not the same, e.g. all
> > > > distances in "dist2.Na3.dat" are ~5 Angstrom larger than those in
> > > > "dist1.Na3.dat". This seems to me that some ions were not properly
> > imaged
> > > > when we used command "image origin center". Or is there any mistake for
> > my
> > > > script file? Any suggestion?
> > > >
> > > >
> > > >
> > > > One more question, is it possible to calculate the distance between
> > each
> > > > Na+ ions and residue#1 using one command line and how? or should I use
> > 18
> > > > command lines of 18 Na+ ions?
> > > >
> > > >
> > > >
> > > > Thank you very much in advance for your kindness.
> > > >
> > > > Best,
> > > >
> > > > Xioling
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
> > > Best,
> > > InSuk Joung
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> > > AMBER.ambermd.org
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> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Best,
> InSuk Joung
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Received on Tue Aug 03 2010 - 21:00:03 PDT
