[gmx-users] Invalid atom number 6415 in indexfile

[Justin A. Lemkul]

Liu Shiyong wrote:
> Hi,
> 
> Did you get my script ?  

As I said just a few days ago, I don't run jobs for people.  I only have 
allocated time on our University's cluster, which I need for myself.

That said, it is also very difficult to go through someone's scripting, laden 
with variables that mean nothing to anyone else but you, and come up with 
something meaningful, especially when everyone on this list has their own work 
to be doing.  As I've said several times, simply posting your command lines with 
the relevant error message(s) is sufficient.

That said, I really have no clue what you're doing with those scripts.  It 
appears that you are running pdb2gmx, grompp, and mdrun, then using trjconv to 
dump out the last frame from your energy minimization.  The last step is 
certainly not necessary; mdrun outputs the lowest-energy coordinates.

Then you are running pdb2gmx again, and creating index groups.  I don't 
understand the purpose of the second pdb2gmx call.

The problem you are facing is easily answered with the fact that you simply are 
again using a structure file that does not have the same number of atoms as the 
structure you used to create the index file.  It appears that your index files 
simply have two chains of a protein, with the highest atom number being 5966. 
So of course atom 6415 is missing.  The simple fix is to perhaps simplify your 
naming strategy so you can keep it straight, or instead of scripting everything 
and potentially making mistakes, to just run the commands interactively until 
you have everything flowing.

-Justin

> I dump a frame from .trr file.
> I did not define xtc-grps
>  
> 
> On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Liu Shiyong wrote:
> 
>         Hi,
> 
>          I got an error when do grompp:   The input PDB file comes from
>         the output of GROMACS by trajconv command.
> 
> 
>     <snip>
> 
>         -------------------------------------------------------
>         Program grompp, VERSION 3.3.3
>         Source code file: ../../../../src/kernel/readir.c, line: 838
> 
>         *Fatal error:
>         Invalid atom number 6415 in indexfile*
>         -------------------------------------------------------
> 
> 
>     Instead of screen dumps, it would be a lot more useful to see your
>     .mdp file, as well as the command line (not output from) both grompp
>     and trjconv.  Did you dump the frame from an .xtc file?  What did
>     you specify in xtc-grps?
> 
>     -Justin
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu 
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab:    http://vakser.bioinformatics.ku.edu/people
> Phone:      (785) 864-1962

-- 
========================================

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

========================================