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

[Yang Ye]

Hi,

Putting ions as individual molecule is quite a standard practice. 
Looking at ions.itp in the top directory. I added ions there with new 
forcefield preprocessor directives. Most gromacs users except you will 
get a low mark, I reckon.

I tried your way in the previous and just now. It works. You may use -pp 
for your grompp and send me directly the output file if you are keen to 
find more.

Yang Ye

D. Ensign wrote:
> numbered consecutively
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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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