[gmx-users] Invalid line in coordinate file

[Justin Lemkul]

On 12/13/12 1:34 AM, Shine Devaraj wrote:
> Dear users,
> I have used grompp command for minimising my protein and ligand in membrane
> after using inflategro command.
> My system has no problem in visualizing in VMD. The protein is in proper
> order
> But I am getting the error
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: confio.c, line: 728
>
> Fatal error:
> Invalid line in system_inf.gro for atom 6835:
> 25.67360 25.77400 6.59650
> -------------------------------------------------------
> .............
>           128DPPC   C46 6396  24.164   0.531   3.551
>           128DPPC   C47 6397  24.158   0.578   3.406
>           128DPPC   C48 6398  24.266   0.510   3.321
> 6835  128DPPC   C49 6399  24.248   0.548   3.174
>           128DPPC   C50 6400  24.346   0.469   3.086
>            25.67360 25.77400 6.59650
>
> Kindly make some light on this.
>

The second line in a .gro file specifies how many atoms there are.  You've 
specified too many, since grompp is looking for atom 6835, but it finds box 
vectors instead.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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