Re: [AMBER] charge derivation for simulations in organic solvents

From: Dr. Vitaly V. G. Chaban <>
Date: Mon, 6 Aug 2012 11:18:06 -0400

You can simulate a cluster of your solvent molecules using some
high-level ab initio method, e.g. MP2, and compare charges to those
from HF (in vacuum!). If you find them more or less concerted, then
use HF (in vacuum). If not, either correct the HF charges somehow or
use the results from MP2 (of several molecules).

It is not an exact methodology, nor MP2 is computationally cheap, but
it is probably the only way to get reliable picture without engaging
physical experiment.


On Mon, Aug 6, 2012 at 11:03 AM, Igor Pochorovski
<> wrote:
> Thanks a lot for your quick reply!
> Do you know whether there is a way to test for the dipole moment increase
> due to electronic polarization, for example in case of chloroform?
> On 06.08.12 16:58, "Dr. Vitaly V. G. Chaban" <> wrote:
>>On Mon, Aug 6, 2012 at 10:53 AM, Igor Pochorovski
>><> wrote:
>>> Dear amber users,
>>> I would like to perform AMBER GAFF simulations of supramolecular
>>>systems in
>>> organic solvents like chloroform, THF, or benzene. The standard method
>>> charge derivation in GAFF is RESP HF/6-31G(d), which is known to
>>> overestimate dipole moments. While this is regarded to be advantageous
>>> simulations in water, I am not sure whether it is the best method for
>>> simulations in organic solvents. On the other hand I obtained
>>>topologies of
>>> the solvent molecules from whose charges have been
>>> determined using a method which gives similar charges as HF/6-31G(d).
>>> Do you think it is OK to use HF/6-31G(d) or would it be better to use,
>>> example, B3LYP/cc-pVTZ that is known to reproduce gas phase charges?
>>This, unfortunately, depends on each particular solvent. HF somewhat
>>overestimates partial charges. If this everestimation is in agreement
>>with the dipole moment increase due to electronic polarization in
>>condensed phase of the solvent/solution, than the method works nice.
>>If not, than large discrepancy can be expected.
>>Dr. Vitaly V. Chaban, 430 Hutchison Hall
>>Dept. Chemistry, University of Rochester
>>120 Trustee Road, Rochester, NY 14627-0216
>>AMBER mailing list

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
AMBER mailing list
Received on Mon Aug 06 2012 - 08:30:02 PDT
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