From owner-chemistry@ccl.net Sat Dec 29 16:20:01 2012
From: "sobereva sobjubao(0)yahoo.com.cn" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: AIMPAC and MORPHY98
Message-Id: <-48032-121229105056-8284-DlF013i0yH0BS+mmxBYMRQ+*+server.ccl.net>
X-Original-From: sobereva <sobjubao ~ yahoo.com.cn>
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Date: Sat, 29 Dec 2012 23:50:44 +0800 (CST)
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Sent to CCL by: sobereva [sobjubao||yahoo.com.cn]
Dear Leonardo,

The quantitative molecular surface analysis module of Multiwfn program can do this. First download its 2.6.1 beta version from http://multiwfn.codeplex.com (at "Recent update history" section), then boot it up and load the corresponding .wfn or .fch file, then select main function 12. Select option 0 to carry out the surface analysis, after that select 10 and input the index of the atom you are interested in, then the closest distance between the isosurface (default setting is rho=0.001) and its nucleus will be immediately outputted on screen.

Note that by default, Multiwfn will analyze electrostatic potential (ESP) on the surface. For large system this task may be time-consuming. In order to reduce the computational time, before choosing option 0 you can select 2 and then select 2 again to choose average local ionization energy (ALIE) instead of ESP. ALIE is quite cheap and therefore the surface analysis step can be finished rather rapidly.

BTW: After the surface analysis step is finished, you can also select option 6 to export all of the points scattered on the surface to a pdb file. Then if you load the pdb file along with the molecular structure file into a visualization program such as VMD, you can manually measure the distance between a nucleus and any region of the surface.

Best wishes,

Tian Lu


--- On Thu, 12/27/12, Leonardo Viana Lima leonardovc.lima^_^gmail.com <owner-chemistry[A]ccl.net> wrote:

> From: Leonardo Viana Lima leonardovc.lima^_^gmail.com <owner-chemistry[A]ccl.net>
> Subject: CCL: AIMPAC and MORPHY98
> To: "Lu, Tian " <sobjubao[A]yahoo.com.cn>
> Date: Thursday, December 27, 2012, 10:54 AM
> 
> Sent to CCL by: "Leonardo Viana Lima"
> [leonardovc.lima###gmail.com]
> Hello, CCL Subscribers.
> 
> I'm studying intramolecular hydrogen bonds using the eight
> Popelier's criteria. 
> 
> I have access to MORPHY98 and AIMPAC to calculate the
> desired proprieties, but 
> in none of them I find out how to calculate the non-bonded
> radius of an atom 
> (the shortest distance of the corresponding nucleus to the
> 0.001 au surface 
> contour). I tried the WALL keyword in MORPHY98 but nothing
> was printed in 
> output file.
> 
> Somebody knows how to calculate the non-bonded radius in any
> of this softwares?
> 
> Thanks in advance.
> Leonardo.
> 
> 
> 
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