[gmx-users] How to specify conection between 2 molecule in the top file?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 6 15:20:38 CEST 2008

Frankie Montenegro wrote:
> Hi everyone, I have a question regarding a forcefield build.
> Is there a way to specify in the topology file how to bond two molecules
>  one to another?

The GROMACS implementation of bonded interactions doesn't permit them 
between atoms in different [ molecules ] sections. What you put in such 
a section, however, is your own business.

> So this thing, a halfaring + carboxyl on the left is one molecule and 
> similar
>  thing on the right is the other molecule. 

No, they are fragments of molecules.

> But I need to bond carbons a 
> and b
>  to get the full ring. Is this possible? Please don't ask me why I 
> didn't make the
> whole thing one molecule (it is convinient for some other reason) I am 
> using my
>  own bonds angles and dihedrals, not "virtual sites" or any of that stuff.
> Is that "+" and "-" stuff from rtp file going to work here? Thanks, Frankie

A measured approach and a respectful tone is always a good idea when 
asking for free advice. If your knowledge of the topology file syntax 
was so good that your assumption (that you don't need to defend part of 
your unusual choice) was actually valid, then you'd know enough to solve 
the problem that it was creating :-)


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