AMBER Archive (2009)

Subject: Re: [AMBER] questions about RESP

From: Jeffrey (
Date: Thu Jul 23 2009 - 07:51:34 CDT

Dear Francois,
   Many thanks. Since the fitted atomic charges are dependent on the conformation used for MEP calculation, we should use the conformation near the one bound in the receptor, which is usually not the minimum. Then why is it necessary to optimize the isolated ligind structure to the minimum to calculate the MEP?  After your detailed explanation, now my main confusion is about how it will affect the fitted atomic charge when we use a conformation not corresponding to the minimum at 6-31G**.
Any paper on this topic on how the non-minimum conformation affect the atomic charges?
Of course, to split a big molecule into pieces is a good choice.
Thanks so much.

--- 09年7月21日,周二, FyD <> 写道:

发件人: FyD <>
主题: Re: [AMBER] questions about RESP
收件人: "AMBER Mailing List" <>
日期: 2009年7月21日,周二,上午4:46

Dear Jeffrey,

> 聽聽聽聽聽 Thanks very much for your information. I read that paper and  make it clear of the different level of optimization. Another  question is that why the structure should be optimized before  calculating ESP?

To define (a) "correct/well-defined/canonical_?" structure/conformation(s) to be used in MEP computation.

> How about a structure near the mimimum point, but  not at the real mimimum when calculating the ESP?

I see... your structure is too big & you cannot reach convergence... Right ?

When we optimize a structure we always use "Tight" convergence, instead of using default convergence criteria to better define the corresponding minimum.

> For large molecules, it is difficult to optimize the structure at  6-31G* level. So how about using a conformation obtained at a low  level optimization?

Did you ever optimize H3O+ (for instance) using HF/3-21G instead of HF/6-31G* ?

When you have a big structure, decreasing the theory level in QM might appear an attractive approach. Others in the list might have different experiences - my feeling is that removing polarization functions for instance will lead to inaccurate structures. HF/6-31G* & HF/6-31G** provide reasonable results for organic and bio-organic structures, and are widely used.

Another problem that shows up when you have a big structure is how rigorously defining the corresponding conformation(s) ? Thus, quite often the conformation(s) selected in this case is(are) are not rigorously defined but rather generated after crude construction & geometry optimization. This might be a problem as conformation strongly affect charge values based on MEP computation.

Thus, I would suggest you to split your big molecule into two or more fragments (with well defined conformations), and use R.E.D. to compute RESP charges & build the corresponding FF libraries.

regards, Francois

>> 聽 聽 聽 If the optimization and ESP calculation are performed at聽  different level, e.g.聽 HF/3-21G for optimization and HF/6-31G* for聽  ESP calculation, how will it effect the fitted atomic charges?
>> Are there any papers or materials discussing this topic?
> You might find some information about that in
> Hariharan, P. C.; Pople, J. A. Chem Phys Lett 1972, 16, 217.

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