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

[Justin A. Lemkul]

lloyd riggs wrote:
> 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

I posted this earlier:

http://pubs.acs.org/doi/abs/10.1021/ci100335w

We did a systematic analysis of several charge calculation methods.  None of 
them could exactly reproduce the Gromos96 charges on any of the molecules 
analyzed, which sort of makes sense, given the empirical nature of Gromos96 
parameterization (estimate charge, fiddle with it until some condensed phase 
properties are right).

-Justin

> 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)
> 
> 
> ----------------------------------------------------------------------
> 
> 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> Message-ID: 
> <F625AF4746B3A74DACFF00F6F65BECCB1C04DBB0 at vPRK-MBX-01.vcp.local> 
> Content-Type: text/plain; charset="us-ascii"
> 
> 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:
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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