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
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > 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
>
--
Best,
InSuk Joung
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Received on Tue Aug 03 2010 - 11:30:06 PDT
