[gmx-users] pair interaction in ligand topology file

David Mobley dmobley at gmail.com
Mon May 29 20:25:27 CEST 2006

Do you mean, "use pair interactions"? If you're referring to the [
pairs ] section of your topology, well, you will probably need to look
at details on the force field to see what it expects, as the answer to
this is force field dependent, and I don't typically use OPLS-AA. The
[ pairs ] section is usually used to modify 1-4 interactions, but can
also be used to modify other interactions if you do things right. This
is explained in the manual.

In terms of generating ligand topologies, there are some programs
which can do this automatically for OPLS, I think. Schrodinger has
one, I believe. Unless you are very well versed in the force field it
might be worthwhile looking into this, as obviously, if  you make any
mistakes in generating your own topology, your results can be garbage.
 If you are not committed to the OPLS force field, it is also
relatively straightforward to automatically generate ligand topologies
using AMBER's GAFF force field. Or prodrg can generate topologies for
some other force fields.

If you are intent on doing it by hand, be sure you know what you are
doing, and be very careful.


On 5/28/06, 4tejender <4tejender at indiatimes.com> wrote:
> Dear Gromacs users,
>  I am tring to bulid ligand topology using OPLSAA forcefield. I want to know that should i user pair interactions in the ligand topology. If yes what is criteria for chosing atom pairs for pair interactions
> with thanks
> teje
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