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 _____________________________ 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: -- NEU: FreePhone - kostenlos mobil telefonieren! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
