AMBER Archive (2005)

Subject: Re: AMBER: Problem in ptraj

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Feb 02 2005 - 12:16:03 CST

Since there's been no word from Thomas, I imagine he's out of play at the
moment. He's usually very prompt to address ptraj questions. If you'd like to
send some of your files to me directly, I can check them out. I didn't write the
code, of course, but I've done the things you're trying to do many times. If you
could also send your sander input file as well as maybe two trajectories, prmtop
and your ptraj input, I'll see if I can duplicate (or figure out!) the problem.

K

Quoting anshul_at_imtech.res.in:

> Dear Kristina,
> > All of this sounds very strange to me. Does your average structure
> > calculated on
> > the compound trajectory you made with nobox look "normal"?
>
> I checked this structure and found that it is not correct. So I think that
> there is something wrong witht he compound mdcrd file created but what it
> is I dont know.
>
>
> > I would anticipate that you would have a problem with the mdcrd file
> > created without nobox, and am surprised that you have been able to use
>
> I checked the individual mdcrd files and generated the average structure
> using each one separately. I found that that the structures thus generated
> are perfectly all right. Also I generated pdb structures for all the
> frames from individual mdcrd files. and these structures are also all
> correct.
>
> I also tried to generate the pdb structures and average structure from the
> individual mdcrd files using the nobox keyword and these structures were
> exactly the same as that generated without the use of nobox.
>
> Can you or Thomas Cheatham or anyone else shed some more light on what
> might be going wrong.
>
> With best regards,
> Anshul
>
> > In the past, if I didn't have a
> > periodic box and I forgot to use the nobox keyword, ptraj would take the
> > xyz coordinates of the first atom of my second frame and use them as box
> > coordinates, then assign the coordinates of the second atom to the first
> > atom, etc. so that my trajectory would end up looking like spaghetti. If
> > yours looks normal without the nobox keyword, then either something
> has > changed or something is wrong.
> > Maybe Thomas Cheatham can shed some more light on this.
> > In the meantime, I would suggest you compare the trajectories as well as
> > your
> > average structures you made different ways in a viewer and see how they
> > compare.
> > Did you move anything when adding the trajectories together? If you just
> > read
> > them in, then wrote them back out as one I don't know why the coordinates
> > are
> > changing.
> >
> > Good luck!
> > Kristina
> >
> > Quoting anshul_at_imtech.res.in:
> >
> >> Dear Kristina,
> >> Thanks for your reply. I used the nobob keyword and was able to get the
> >> average structure. but now i face anotherproblem when i tru to use the
> >> mdcrd file thus created to generate the pdb files for all the frames.
> >> the
> >> x y z coordinates of these files are too large and some even have
> >> *******
> >> at many places. Onthe other hand Iif I use the mdcrd file created
> >> without
> >> using the nobox keyword, the generated pdb files seem to be ok. Do you
> >> have any suggestions for this?
> >> Thanks once again.
> >> With best regards,
> >> Anshul
> >>
> >> -------------------------------------------------
> >> Anshul Awasthi
> >> Bioinformatics Center
> >> Institute of Microbial Technology
> >> Chandigarh, India.
> >> Mobile +91-9872220352
> >> -------------------------------------------------
> >>
> >> On Mon, 31 Jan 2005, Furse, Kristina Elisabet wrote:
> >>
> >> > Try using the nobox keyword for your trajout line since you do not
> >> have a
> >> > periodic box:
> >> >
> >> > trajout grp3.mdcrd nobox
> >> >
> >> > Good luck,
> >> > Kristina
> >> >
> >> >
> >> > Quoting anshul_at_imtech.res.in:
> >> >
> >> > > Dear Amber users,
> >> > > I have done MD simulations ona protein using GB model. Since my
> >> process
> >> > > war restarted a few times so I used Ptraj to combine the mdcrd files
> >> and
> >> > > made a new one. then I used this file to get an average structure
> >> but
> >> got
> >> > > this error:
> >> > > ------------------------------------------------------
> >> > > Processing AMBER trajectory file bsa-grp3.mdcrd
> >> > >
> >> > > Set 1 .................................................
> >> > > Set 50 ........................................
> >> > > ERROR in readAmberTrajectory(): fsetpos() failed on when looking for
> >> box
> >> > > coordinates!
> >> > > -----------------------------------------------------
> >> > >
> >> > > In all there are 179 frames and I have not used any periodic box
> >> > > conditions. If I run the same script of ptraj for indovidual mdcrd
> >> files,
> >> > > I get the average structure. the new combined mdcrd file works well
> >> for
> >> > > other kinds of analysis.
> >> > >
> >> > > The ptraj script for getting the average structure is:
> >> > >
> >> > > ptraj mod9.prmtop << EOF
> >> > > trajin grp3.mdcrd
> >> > > average grp3-avg-pr.pdb PDB
> >> > > EOF
> >> > >
> >> > >
> >> > > and the one to combine the mdcrd files is:
> >> > >
> >> > > ptraj mod9.prmtop << EOF
> >> > > trajin gbmd-pr.mdcrd
> >> > > trajin gbmd-pr-1.mdcrd
> >> > > trajin gbmd-pr-2.mdcrd
> >> > > trajin gbmd-pr-3.mdcrd
> >> > > trajin gbmd-pr-4.mdcrd
> >> > > trajin gbmd-pr5.mdcrd
> >> > > trajout grp3.mdcrd
> >> > > EOF
> >> > >
> >> > >
> >> > > Can anyone tell me where I am going wrong and how to rectify the
> >> problem.
> >> > >
> >> > > with Thanks and best regards,
> >> > > Anshul
> >> > >
> >> > >
> >> > > -------------------------------------------------
> >> > > Anshul Awasthi
> >> > > Bioinformatics Center
> >> > > Institute of Microbial Technology
> >> > > Chandigarh, India.
> >> > > Mobile +91-9872220352
> >> > > -------------------------------------------------
> >> > >
> >> > >
> >> > >
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> >> > >
> >> >
> >> >
> >> > -----------------------------------------------------------------
> >> > Kristina E. Furse
> >> > Department of Chemistry
> >> > Center for Structural Biology
> >> > Vanderbilt University
> >> > Email: kristina.e.furse_at_Vanderbilt.Edu
> >> > -----------------------------------------------------------------------
> >> > The AMBER Mail Reflector
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> >> >
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> >
> >
> > -----------------------------------------------------------------
> > Kristina E. Furse
> > Department of Chemistry
> > Center for Structural Biology
> > Vanderbilt University
> > Email: kristina.e.furse_at_Vanderbilt.Edu
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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