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 <junmwang.gmail.com>:
>
> 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 <david.case.rutgers.edu>
> 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
