[gmx-users] How to use ambconv package...

[Tomas Kubar]

Hi Dave

david.evans at ulsop.ac.uk wrote:
> Hi, Tomas,
> 
> Are you using ambconv regularly?

Yes. Predominantly for isolated bases and DNA duplexes.

> I managed to get it working, but was
> slightly concerned that the energies between AMBER and Gromacs did
> not agree so well (~1% difference for isolated DNA duplex, ~10% for
> VdW in a solvated DNA duplex), compared to Filip Ryjacek's stated
> accuracy of 0.01%. I was wondering if you had managed to get better
> accuracy.

I did not test it as properly as you did, I guess. Could you desribe 
your tests in more detail to make me able to reproduce them? I suppose 
you are talking about interaction energy..

Thank you
tomas