<P>
Hi Tsjerk,<BR>
You have cleared my doubts. I had fitted the structures in the pdb files, which is <BR>
why I was confused because different coordinates were encountered for the same time step <BR>
in the original and extended run( that had crashed).<BR>
Now I understand, where lies the problem.<BR>
<BR>
Thank you very much.<BR>
<BR>
Sarbani<BR>
<BR>
<BR>
On Thu, 11 Sep 2008 Tsjerk Wassenaar wrote :<BR>
>Hi Sarbani,<BR>
><BR>
>If you only want to extract coordinates from your trajectory it does not matter.<BR>
><BR>
>The trajectory file (.xtc) only contains coordinates. To make a<BR>
>pdb/gro/whatever file from it, you need to add information regarding<BR>
>atom/residue names, etc. That will be taken from a pdb/gro/tpr file,<BR>
>but will be the same for an initial or restart .tpr file.<BR>
><BR>
>The pdb/gro/tpr file contains an atom list together with coordinates,<BR>
>and a .tpr file also contains topology information (masses, charges,<BR>
>bonds, angles, etc.). When using trjconv, this information may be used<BR>
>for fitting and for some pbc related operations. In that case it will<BR>
>matter which .tpr file you use for reference, since fitting against<BR>
>the initial set of coordinates will yield results different from a fit<BR>
>against coordinates from the end or midway a run. Options like -pbc<BR>
>nojump add further restrictions to the reference file you use, but for<BR>
>that do browse the archives, as I don't feel like elaborating on that<BR>
>again.<BR>
><BR>
>Cheers,<BR>
><BR>
>Tsjerk<BR>
><BR>
>On Thu, Sep 11, 2008 at 8:12 AM, sarbani chattopadhyay<BR>
><sarbani_c84@rediffmail.com> wrote:<BR>
> > Hi everyone,<BR>
> > I am facing a peculiar problem.<BR>
> ><BR>
> ><BR>
> > I had given an exteneded continuation run using the "tpbconv" command.<BR>
> ><BR>
> > The extended run had crashed due to power failure. I again gave an exact<BR>
> > continuation run<BR>
> > using the "tpbconv" command.<BR>
> ><BR>
> > After the run was over, I concatenated the trajectory files using "trjcat"<BR>
> > command.<BR>
> ><BR>
> > My question is that which ".tpr" file should I use when I use the "trjconv"<BR>
> > command to generate<BR>
> > the pdb file from the trajectory ie. should I use "extended.tpr" or<BR>
> > "restart.tpr ".<BR>
> ><BR>
> > Thanking You,<BR>
> > Sarbani<BR>
> ><BR>
> ><BR>
> ><BR>
> > _______________________________________________<BR>
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> ><BR>
><BR>
><BR>
><BR>
>--<BR>
>Tsjerk A. Wassenaar, Ph.D.<BR>
>Junior UD (post-doc)<BR>
>Biomolecular NMR, Bijvoet Center<BR>
>Utrecht University<BR>
>Padualaan 8<BR>
>3584 CH Utrecht<BR>
>The Netherlands<BR>
>P: +31-30-2539931<BR>
>F: +31-30-2537623<BR>
</P>
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