Re: [AMBER] Wrong connectivity after antechamber/Gaussian16

From: Andreas Tosstorff <>
Date: Sat, 28 Oct 2017 22:47:33 +0200

thank you both for your responses! which basis sets would you recommend using when using a solvent model? my understanding is that HF6-31g* tends to exaggerate polarization, which is why people use it when calculating charges in the gas phase to be then applied in MD in solution.

Von meinem iPad gesendet

> Am 28.10.2017 um 15:23 schrieb Junmei Wang <>:
> Good point. I encountered the same problem when I optimized amino-acid-like
> small molecules using Gaussian. The optimizer in the recent Gaussian
> versions can migrate proton from one heavy atom to another to neutralize
> the molecule. The two atoms may be separated several bonds (the longest
> distance is 7 bonds)! My solution was to use PCM to do optimization and
> then did a single point calculation to calculate ESP. With PCM, the charge
> centers are well kept.
> Best
> Junmei
> On Sat, Oct 28, 2017 at 8:16 AM, David A Case <>
> wrote:
>>> 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.)
>> ....dac
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Received on Sat Oct 28 2017 - 14:00:01 PDT
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