[gmx-users] Invalid atom number 6415 in indexfile

[Liu Shiyong]

Hi,

Did you get my script ?
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> 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 | (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 (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962
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