Thanks for the advice! This worked!
On 10/29/2017 02:02 AM, Junmei Wang wrote:
> I usually use B3LYP/6-31G* SCRF=PCM to do geometry optimization and then
> calculate ESP at HF/6-31G* level to be consistent with GAFF and some
> biomolecular force fields.
>
> Best
>
> Junmei
>
>
> On Sat, Oct 28, 2017 at 4:47 PM, Andreas Tosstorff <
> andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
>> 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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--
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Tue Nov 07 2017 - 02:30:02 PST
