Re: [AMBER] Wrong connectivity after antechamber/Gaussian16

From: David A Case <>
Date: Sat, 28 Oct 2017 08:16:25 -0400

On Sat, Oct 28, 2017, Andreas Tosstorff wrote:

> Thanks a lot for the advice! The structure I have is that of the small
> molecule bound to a protein. If I submitted this structure, without
> further geometry optimization, wouldn’t that overstabilize the bound
> ligand conformation?

In principle, MD results should become independent of the starting
configuration as sampling becomes more complete.

>From the point of view of developing charges, many people prefer to fit
several conformations at once, to get kind of an "average" charge set that
works pretty well for many conformations. The ways in which those
conformations are generated is outside the scope of antechamber/resp.

You might try adding a cosmo solvation model to the Gaussian run, then
optimizing. The will probably stabilize the zwitterionic form. Or, minimize
the molecule in a force field, since that is what you will be using for the
binding calculation anyway. (This is iterative: get charges for
the conformation you have, minimize in ff, re-determine charges from this
minimized conformation, see if they have changed very much.)


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Received on Sat Oct 28 2017 - 05:30:02 PDT
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