Re: [AMBER] positive free energy

From: David A Case <>
Date: Wed, 20 Aug 2014 14:48:37 -0400

On Wed, Aug 20, 2014, zahra khatti wrote:
> I obtained positive free energy from
> In my case the receptor and ligand didn't joint together. The distance between them
> is about 1-2 angstrom. Is this  related to positive free energy?

I don't think people can help much from long distance. Note that Amber (and
other MM programs) do not create covalent bonds just because atoms are close
together; the bonds are specified in the process of setting up the topology.

If you have a distance between (atoms of???) the receptor and ligand that are
"about 1-2 angstrom", you need to think about whether or not there is supposed
to be a chemical bond. And you will need to add it if there is. Note that
mmpbsa is designed for the analysis of non-covalent interactions, and won't
work if you are looking at covalent binding.

Note also the use of mmpbsa is an *advanced* topic in simulation. Be sure you
know how to run simpler things, and know how to visualize simulation results
and can create an informed opinion about its quality. If you have not done
so, be sure you can carry out some simple binding calculations and get good

People on the mailing list will try to help if they can, but you need to
provide enough information and ask specific questions.

...good luck....dac

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Received on Wed Aug 20 2014 - 12:00:03 PDT
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