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.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.Vanderbilt.Edu
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
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Received on Tue Feb 01 2005 - 12:53:00 PST
