[gmx-users] RE: Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

[lloyd riggs]

I also found this usefull, but have a question on what one would consider the standard.  from eyeballing mostly the charges I get for .itp files from PRODRG server fall into mullikin charges, but usually 3-4 dont or have no charge, but I woundered if the ESP or AIM charges would be beter.  From the web page http://cccbdb.nist.gov/ which gives an overload of charge, angle etc tables and how they were determined.

ESP	Electrostatic potential. The electrical potential due to the nuclei and electrons in the molecule, as experienced by a test charge.

AIM	Atoms-in-molecules. An analysis method based upon the shape of the total electron density; used to define bonds, atoms, etc. (5). Atomic charges computed using this theory are often quite different from those from other analyses (e.g., from Mulliken populations). Such charges are probably the most justifiable theoretically, but meet some resistance because the values obtained may be quite different from those from older theories (6).

In addition, how would AIM charges play out in Gromacs, especially with center points in rings which are different from nuclear centers, but representative of PI orbitals, etc...With some say dummy point lacking geometry (not that I would ever do that, but I do often wounder about representation of PI interactions in simulations, such as say a metal ion trapped between two benzene rings by PI)

And as an example, this is a partial table of a molecule--


Computed charges for C6H5NH2 (aniline)

HF/3-21G

 	Charge (e)
Number	Element	Mulliken	chelpg	AIM	ESP
1	C	0.390	 	 	0.715
2	C	-0.269	 	 	-0.486
3	C	-0.211	 	 	-0.037
4	C	-0.278	 	 	-0.316
5	C	-0.211	 	 	-0.037
6	C	-0.269	 	 	-0.486
7	N	-0.984	 	 	-1.143
8	H	0.224	 	 	0.203
9	H	0.236	 	 	0.152
10	H	0.229	 	 	0.171
11	H	0.236	 	 	0.152
12	H	0.224	 	 	0.203
13	H	0.341	 	 	0.453
14	H	0.341	 	 	0.453

Basically, I woundered which would be more proper charge wise in constructing small, or medium sized molecules.

Stephan Watkins
--Sorry its an answere with a question attached.


Today's Topics:

   1. RE: Umbrella sampling of phosphate ion binding (Dallas Warren)


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Message: 1
Date: Thu, 09 Jun 2011 01:30:34 +0000
From: Dallas Warren <Dallas.Warren at monash.edu>
Subject: RE: [gmx-users] Umbrella sampling of phosphate ion binding
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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You have been provided there with the reference in which the parameters for the molecule were derived.

Read it!

And determine yourself if it is applicable or not to what you are doing and the forcefield you are using.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of bharat gupta
Sent: Thursday, 9 June 2011 11:29 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Umbrella sampling of phosphate ion binding

I found it in the /shared/top/ gmx.ff folder . Here's the file

;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
[ moleculetype ]
; name  nrexcl
h2po4    4

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
; use charges from Janez Mavri
     1      OA       1     PI       O1       1        -0.777
     2      OA       1     PI       O2       1        -0.777
     3      OM       1     PI       O3       1        -0.943
     4      OM       1     PI       O4       1        -0.943
     5       P       1     PI        P       1         1.596
     6      HO       1     PI       H1       1         0.422
     7      HO       1     PI       H2       1         0.422

[ bonds ]
;  ai    aj funct           c0           c1
    5     1     1 1.637000e-01
    5     2     1 1.637000e-01
    5     3     1 1.478000e-01
    5     4     1 1.478000e-01
    6     1     1 0.943000e-01
    7     2     1 0.943000e-01

[ angles ]
;  ai    aj    ak funct           c0     c1
    2     5     1     1 1.015000e+02     400
    3     5     1     1 1.059000e+02
    4     5     1     1 1.082000e+02
    3     5     2     1 1.059000e+02
    4     5     2     1 1.082000e+02
    4     5     3     1 1.248000e+02
    6     1     5     1 1.082000e+02
    7     2     5     1 1.082000e+02

[ dihedrals ]
;  ai    aj    ak    al funct
    6     1     5     2     1
    7     2     5     1     1

Can I use it or not ??
On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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