[gmx-users] topology

[Erik Lindahl]

Hi,

You may not like this, but especially for a small  molecules that are
> non-standard you have to check manually whether the toplogy makes 
> sense.
> This is your research and you have to be able to explain why you have
> used such and such parameters.
>

This cannot be stressed enough.

There are programs like Macromodel/batchmin that try to perform an 
automatic assignment of parameters. Unfortunately, my experience is 
that there are very often
errors in these assignments, even when Macromodel claims it is only 
using "high quality parameters".

The last time I checked a Macromodel topology the program didn't even
check that the system was neutral, but it had chosen parameters that 
gave a charge of +0.6 for a ~30 atom hydrocarbon.

Cheers,

Erik