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
<[email protected]> Subject: RE: [gmx-users] Umbrella sampling of
phosphate ion binding To: Discussion list for GROMACS users
<[email protected]> Message-ID:
<[email protected]>
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 [email protected] +61 3 9903 9304
--------------------------------- When the only tool you own is a hammer,
every problem begins to resemble a nail.
From: [email protected] [mailto:[email protected]] On
Behalf Of bharat gupta Sent: Thursday, 9 June 2011 11:29 AM To:
[email protected]; 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
<[email protected]<mailto:[email protected]>> 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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