[gmx-users] invalid line

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 5 20:33:48 CEST 2011

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.


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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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