[gmx-users] Re: grompp: Atoms in the .top are not

D. Ensign densign at stanford.edu
Thu May 4 03:37:01 CEST 2006

numbered consecutively
References: <20060503232617.038DF24857 at xray.bmc.uu.se>
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Regarding addition of ions, apparently resulting in grompp error: Atoms in the .top are
not numbered consecutively from 1
> Try this:
> 1. Paste this at the place of my_ions.itp to replace it.
> [ moleculetype ]
>  NA+             1
>  [ atoms ]
> 1       amber99_31  1       NA+             NA+      1      1    22.99000
> [ moleculetype ]
> CL-             1
> [ atoms ]
> 1       amber99_30  1      CL-             CL-       1      -1   35.45000
> 2. Replace "Ions  1" with
> Na+ 6
> Cl- 2

Why, yes, that seems to work. How interesting.

However, your solution suffers from the problem that it is much simpler and easier to
implement than mine. You get an A-. ;)

Seriously, though, this is interesting. When I run genion on a system, then afterwards
rebuild it with pdb2gmx, it places the ions before the solvent, and places their
topologies in topol_B.itp. Further, in topol_B.itp they are listed as one "molecule" with
no bonds, and indicated in topol.top as one "molecule."

Your solution, on the other hand, makes each ion its own molecule. I like it, but I'm
wondering what's going on.

Dan Ensign
Stanford University

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