AMBER Archive (2009)
Subject: Re: [AMBER] questions about RESP
From: Jeffrey (jeffry20072008_at_yahoo.cn)
--- 09年7月21日，周二, FyD <fyd_at_q4md-forcefieldtools.org> 写道：
> 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.
>> 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?