[gmx-users] abnormal RMSD

[Justin A. Lemkul]

The reason I commented about the use of your .tpr file is that, from your
message, it seemed that you did not understand exactly how to use trjconv, and
were perhaps using a different .tpr file (named topol.tpr) to simply satisfy
trjconv.  Your previous message said your grompp output produced a md.tpr file,
which is what you should be using to conduct your analysis, and was what I was
trying to clue you in on.

In order to get useful help, you must provide information that is
self-consistent, otherwise we are to assume that you are shooting in the dark,
so to speak.  Also, take note of Tsjerk's message from earlier this morning;
his advice about choosing the correct group for output is important.

-Justin

Quoting Anamika Awasthi <aawasthi28 at gmail.com>:

>  Justin I already tried this
>
> I tried this command--->
>
> trjconv -f myprotein.trr -o trajout_whole.trr -pbc  whole
>
>  this was showing this error
>
>  "can not open file
>                topol.tpr"
>  then
> I repeated the same command with "-s topol.tpr"
>
> then
>
> trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump
>
> then
>
> g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr
>
> but now this is showing Fatal Error
>
> " Molecule in topology has atom numbers below and above natoms. you are
> probably trying to use a trajectory which does not match the first 330 atoms
> of the run input file. You can make a matching run input file with tpbconv."
>
> with regards
>  Anamika
>
>
>
>
>
> --
> Anamika Awasthi, PhD
> DBT-Postdoctoral Fellow
> Laboratory of Structural Biology
> Centre for DNA Fingerprinting and Diagnostics (CDFD)
> ECIL Road, Nacharam
> Hyderabad 500 076
> INDIA
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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