AMBER Archive (2003)

Subject: Re: AMBER: Lone pairs and resp

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Nov 17 2003 - 20:06:57 CST

Dear Perdita Barran,
 
> What is not clear in this procedure is where the lone pairs are
> introduced. Are
> dummy atoms made for the lone pairs before carrying out the ESP
> procedure in
> Gaussian? Or is the Gaussian output file modified to include the lone
> pairs?
 
I think :
- first a QM Molecular Electrostatic Potential must be obtained without LP,
- then, this file has to be converted into the RESP format (see Amber7.pdf file P262, section
"input of ESP's and coordinates")
- LPs are added in this RESP file in the section described in "-2nd 2->natoms+1lines-" (see
again page 262) 'by hand' at the place (set of Cartesian coodinates) you decide (be aware of
the units used in this section...)
- Then, you run RESP with these new 'extra-points' using RESP inputs where these
extra-points are set up (see below)....
 
Our program RED does exaclty what I described above but the extra-points are NOT yet
handled. It means if you want to use our prog RED, you have to add extra-points by hand...
 
> Further, how does one declare the lone pair charge points in the RESP
> procedure?
 
In RESP inputs, only the total number of electrons is used... (See 'Amber7.pdf' file, page 261
section "-6th area-") So I guess you should used "zero" for these extra-points... (or try
something else to see if you observe a difference...)
 
> These are defined as 'EP' in the LeAP libraries (e.g.
> all_amino02EP.lib), but this annotation is not recognised by
> antechamber. (Does
> this mean that one uses 'DU' as a dummy atom instead of 'EP').
 
Are you sure Antechamber can handle extra-points ?
 
Best regards, Francois
 
F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm

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