[gmx-users] i can not simulate box of water,

Justin Lemkul jalemkul at vt.edu
Tue Sep 25 19:36:50 CEST 2012

On 9/25/12 11:15 AM, Ali Alizadeh wrote:
> Dear All users
> I made ​​a box of water molecules(w.pdb to w.gro by pdb2gmx then i
> used genbox for made a box), but the grompp did not identify
> molecules(water mode SPC),
> error:
> atom 5721 in wbox.top does not match with in wbox.gro
> atom 5722 in ...............,
>     .
>     .
>     .

These do not look like the actual error messages.  Please copy and paste from 
the terminal rather than retyping and paraphrasing.  Likely the atoms are out of 
order with respect to the topology and you're getting name mismatches, but this 
should not be the case if pdb2gmx produced the coordinate file.



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


More information about the gromacs.org_gmx-users mailing list