The last broken sentence is my mistake. Please ignore that.
On Tue, Aug 3, 2010 at 2:04 PM, InSuk Joung <i.joung.gmail.com> wrote:
> 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
>>
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>
>
>
> --
> Best,
> InSuk Joung
>
--
Best,
InSuk Joung
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Received on Tue Aug 03 2010 - 11:30:10 PDT
