[gmx-users] invalid line

[Justin A. Lemkul]

sarah k wrote:
> dear gromacs users,
> 
> I'm solvating my protein in nitrogen box. I have changed my
> spc216.gro, spc.itp and spce.itp files. I face the following error.

Changed?  In what way?  If you're solvating with nitrogen, why are you dealing 
with water coordinates and topologies?

> How can I fix it?
> 
> invalid line in /usr/share/gromacs/top/spc216.gro for atom 407:
>       0.41200  0.41200  0.41200
> 

In spc216.gro, there are 648 atoms.  If you've somehow manipulated that file 
such that it contains fewer atoms (or something else entirely), whatever Gromacs 
tool you're using will anticipate 648 atoms.  It seems that instead of atom 407, 
it's finding the box vectors.

-Justin

> thanks in advance.
> 
> Best regards,
> Fatemeh Keshavarz
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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