Dear Dr. Jason
Thanks so much, it is working now, and sorry this tiny mistyping
Thanks again.
W. Flak
--- On Fri, 8/27/10, Jason Swails <jason.swails.gmail.com> wrote:
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] ptraj help
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, August 27, 2010, 12:39 AM
> Hello,
>
> I've put comments below:
>
> On Thu, Aug 26, 2010 at 7:58 PM, William Flak <williamflak.yahoo.com>
> wrote:
>
> > Dear AMBER
> > During my data analysis, I had two problems with ptraj
> and couldn't
> > overcome them.
> > 1- Snapshot extracting: when I extracted a snapshot
> from my MD simulation,
> > I got a structure half of my protein is out of the
> water box, I have done
> > refit and image options.
> > ****
> > trajin Step1.mdcrd
> > trajin Step2.mdcrd
> > trajin Step3.mdcrd
> > trajin Step4.mdcrd
> > center :1-223
> > mass origine
> >
>
> This should be mass origin, not mass origine, and it should
> be on the same
> line as the "center" command.
>
> center :1-223 mass origin
>
> image origin center
> > trajout Combined.mdcrd
> > *****
> > 2- Average structure:
> > I had a 2ns simulation length partitioned on 4 mdcrd
> files. I combined
> > these 4 mdcrd files and centered it using ptraj. I
> wanted to get the average
> > strututre of the simulation. I got a structure with
> some groups
> > cross-linked. These groups are free rotated groups
> e.g. CH3 group. is that
> > right? or I made something wrong? How can I solve this
> problem in order to
> > use the average structure for QM/MM optimization.
> > Here is my ptraj command:
> >
> >
> > trajin Step1.mdcrd
> > trajin Step2.mdcrd
> > trajin Step3.mdcrd
> > trajin Step4.mdcrd
> > center :1-223
> > mass origine
> > image origin center
> > trajout Combined.mdcrd
> >
> > ***********
> > trajin Combined.mdcrd
> > strip :WAT
> > average average_structure.pdb pdb
> >
>
> You should do an RMS before you average. Note that
> the manual says that
> average does NOT implicitly RMS. However, you will
> see groups like CH3's
> and carboxylate groups that have free rotation have atoms
> that effectively
> "collapse" into one another since their average location is
> the same (you
> can think of them as being rotationally degenerate in a
> local sense). It is
> quite unlikely that the average structure will be
> appropriate for a QM/MM
> optimization. I think your better option is to
> cluster and pull whatever
> "representative" structure you deem most important.
> The literature may help
> here as well, as may future commentators.
>
> Good luck!
> Jason
>
> **********
> >
> > Any kind of help would be highly appreciated
> > Thanks in advance
> > W. Flak
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 26 2010 - 20:00:04 PDT
