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
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Received on Mon Jan 31 2005 - 17:53:00 PST
