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

Frankie Montenegro frankie.montenegro at gmail.com
Sun Apr 6 16:06:03 CEST 2008

Dear Mark,

I can most certainly express myself in an exteremely dry and stuffed up
manner if it is more to your liking. It seems that my previous 20 postings
weren't critized at all ,even though my posts were utterly  incomprohensible
and my english apolling. But
I promiss to do  my absolut best and from now on my post will contain only
the utmost

Would you be kind to clearify the second part  of  may question? Namely,
could "+" and  "-" signs, mentioned in the manual and used in the rtp files
be helpfull to me
in this case?

Yours Gratefully,
Frankie Montenegro

On Sun, Apr 6, 2008 at 6:20 AM, Mark Abraham <Mark.Abraham at anu.edu.au>

> 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 :-)
> Mark
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