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

[lloyd riggs]

Thank you for the advice Dr. Warren,

I often find the same problem with charges and parameters, and have pulled some from the web in some instances.  I have an old CRC book with tables when in doubt, 

But I wounder if anyone is interested in just making a tabulation, or wiki site to deposite these things when found, as often I feel there would be no references of the sources especially if pulled off of the web (although most parameters can be found in the gromacs entries), but there exist a large amount of difference if people are into accuracy from standardized/averidged to individual molecules (such as C with 3 bonds but 90 Vs 110 degree angles, and differences in charge due to atoms 2-3 bonds downstream or more for larger metals) but I have found these only vary in the 0.00X range usualy, but sometimes an order of magnitude more (just from looking).

I do wounder though about this;

I have used the PRODRG site a few times with compounds that change only a few atoms say on the oposite side of a molecule with 25-30 atoms, and found sometimes I get an .itp file with 0.000 charge for say an NH2 (all 3 atoms), and the charges of 0.076, -0.019 the next, then 0.03 and -0.007 the next and often woundered why?

Stephan Watkins


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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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