AMBER Archive (2005)

Subject: Re: AMBER: Problem in ptraj

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Feb 01 2005 - 13:30:53 CST

All of this sounds very strange to me. Does your average structure calculated on
the compound trajectory you made with nobox look "normal"? 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 it. 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
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