From JF@ctch20.itc.tu-clausthal.de Sun Dec 17 03:48:42 1995 Received: from ctch02.itc.tu-clausthal.de for JF@ctch20.itc.tu-clausthal.de by www.ccl.net (8.6.10/950822.1) id DAA09880; Sun, 17 Dec 1995 03:40:58 -0500 Received: from ctch20.itc.tu-clausthal.de by ctch02.itc.tu-clausthal.de (AIX 3.2/UCB 5.64/4.03) id AA11853; Sun, 17 Dec 1995 16:27:12 +0100 Received: from VARRAN/MAIL by ctch20.itc.tu-clausthal.de (Mercury 1.21); 17 Dec 95 09:39:46 +1 Received: from MAIL by VARRAN (Mercury 1.21); 17 Dec 95 09:39:34 +1 From: "J. Fleischhauer" To: chemistry@www.ccl.net Date: Sun, 17 Dec 1995 09:39:32 GMT+1 Subject: charge equilibration Priority: normal X-Mailer: Pegasus Mail v3.1 (R1a) Message-Id: <2F086539DB@ctch20.itc.tu-clausthal.de> Dear Netters In our approach to describe charge influences in Force Field calculations, we want to try the an empirical method so called (QEq), described in : A. K. Rappe, W. A. Goddard, J. Phys. Chem., 95, 3358, 1991. This method is also available in the commercial CERIUS2 package. Our problem is that there is no detailed description of the algorithm. Does anybody knows other sources of information dealing with the charge equilibration algorithm? Especially we can't find an mathematical expression used for the calculation of the coulomb potential between center A and B = Jab(R). The Problem is the following : The simple coulomb expression between unit charges on center A and B separated by the distance R is : (14) Jab(R) = 14.4 / R 14.4 conversion factor, R in Angstroem, Jab in eV Equation (14) is no longer valid for atoms with overlapping charge distributions (e.g. mostly bonded atoms). For R = 0 (14) leads to an infinite value whereas Jab(R=0) should reach a finite value Jaa instead. Like described in the reference, they use a shielding corrections to (14). The shielding to (14) will be quite large for bonded atoms (small R). The shielding correction to (14) were described in terms of a coulomb integral between atomic densities witch are expressed in form of slater orbitals. (eq.15) (15) Phi_slater = Nn * r power( n-1 ) * exp(-zeta*r) Nn normalisation constant n long periodic row zeta Slater exponent r distance The diatomic Coulomb integral Jab is evaluated exactly. Our question : 1) Witch is the correct mathematical expression to describe the coulomb interaction Jab(R) to get a potential with a finite value for R=0 ? _________________________________________________ Dipl. Chem. Juergen Fleischhauer Technical University Clausthal Dept. of Technical Chemistry Erzstr. 18 D-38678 Clausthal Zellerfeld Germany Tel. : 05323-72-2647 Fax. : 05323-72-3655 E-Mail : jf@ctch20.itc.tu-clausthal.de __________________________________________________ From chpajt@bath.ac.uk Sun Dec 17 04:48:42 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.10/950822.1) id EAA10061; Sun, 17 Dec 1995 04:44:58 -0500 Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Sun, 17 Dec 1995 09:44:53 +0000 Date: Sun, 17 Dec 1995 09:44:50 +0000 (GMT) From: A J Turner To: CHEMISTRY@www.ccl.net Subject: Re Charmm - alpha carbons constraint Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I have a large interest in constraining alpha-carbpns during minimisations. Basically I want to prevent Charmm from trying to change the bulk structure of the enzyme - just the small scale structure. Does anyone have experiance of this - what sort of constraint would be best - and maybe if there is an easy way on defining the selection. Oh - thanks for the units interconversion stuff - I am totally snowed under with your generous replies. Cheers Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From owner-chemistry@ccl.net Sun Dec 17 16:03:51 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA13065; Sun, 17 Dec 1995 15:58:06 -0500 Received: from nic.cerf.net for dgregory@biosym.com by bedrock.ccl.net (8.7.1/950822.1) id PAA22902; Sun, 17 Dec 1995 15:58:03 -0500 (EST) Received: from biff.biosym.com (biff.biosym.com [146.202.0.225]) by nic.cerf.net (8.6.10/8.6.9) with SMTP id MAA27392 for ; Sun, 17 Dec 1995 12:57:57 -0800 Received: from [146.202.14.3] by biff.biosym.com (4.1/SMI-4.1) id AA21805; Sun, 17 Dec 95 12:54:03 PST Message-Id: <9512172054.AA21805@biff.biosym.com> Date: Sun, 17 Dec 1995 13:00:04 -0500 To: chemistry@ccl.net From: dgregory@biosym.com (Don Gregory) X-Sender: dgregory@146.202.0.225 Subject: Re: CCL:Re Charmm - alpha carbons constraint On Dec 16th, A J Turner wrote: > I want to prevent Charmm from trying to change >the bulk structure of the enzyme - just the small scale structure. > >Does anyone have experiance of this - what sort of constraint would be >best - and maybe if there is an easy way on defining the selection. > A J, I would recommend using a harmonic restraint to hold the alpha-carbons *close* to their current positions, but allowing them some flexibility. Of course, the easy thing to do, is to *fix* the atoms in space, this can be done with: CONS FIX SELE TYPE CA END Assuming, of course, all the alpha carbons are named CA. Restraining with the harmonic potential is just as easy, as long as one knows the force constant to apply. CONS HARM SELE TYPE CA END FORCE 100.0 Determining the force constant depends on what forces (energy) you want to counter-balance with the restraint. For example, if you want to make sure the restraint can counter any opposing bond stretching, you might want to apply a counter restraint such that if the alpha carbon moves 1 Angstrom away from its current position, it would impose a restraint of 100 kcal/mol, analogous to bond stretching. To do this, simply apply a force constant of 100. This is what I've done in the above example; a complete description of these CHARMm commands can be found in the "data/doc" directory if you have an installation of Quanta. Alternatively, you can see these commands via the web, looking at the support pages of "http://www.msi.com". Don Gregory From owner-chemistry@ccl.net Sun Dec 17 19:03:53 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA13969; Sun, 17 Dec 1995 18:51:08 -0500 Received: from Ladyhawk.Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by bedrock.ccl.net (8.7.1/950822.1) id SAA23573; Sun, 17 Dec 1995 18:51:05 -0500 (EST) From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HYY6PFXLDC9AMRSB@Levels.UniSA.Edu.Au> for chemistry@ccl.net; Mon, 18 Dec 1995 10:20:18 +0930 Date: Mon, 18 Dec 1995 10:20:18 +0930 Subject: summer schools in Europe? To: chemistry@ccl.net Message-id: <01HYY6PFZ78I9AMRSB@Levels.UniSA.Edu.Au> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, Does anybody know of any summer schools in quantum chemistry/ molecular modelling that are taking place in the coming summer in Europe? I know there was one last year in Italy. Is this an annual event? Thanks Andrea From arthur_j@chem.usyd.edu.au Sun Dec 17 19:14:16 1995 Received: from lars.chem.su.oz.au for arthur_j@chem.usyd.edu.au by www.ccl.net (8.6.10/950822.1) id SAA13976; Sun, 17 Dec 1995 18:55:25 -0500 Received: (from arthur_j@localhost) by lars.chem.su.oz.au (8.6.9/8.6.9) id KAA17068; Mon, 18 Dec 1995 10:55:15 +1100 Date: Mon, 18 Dec 1995 10:55:13 +1100 (EDT) From: Jonathan Arthur Subject: SUMMARY: Fortran debugger To: Computational chemistry list Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Recently I posted the following query: >Does anyone know of a good (and free!) utility to assist in debugging >Fortran programs? (For UNIX) > >And if so where can I get it from? The following is a summary of the responses that I receieved to the query for those who are interested. Now all that remains is to decipher how these programs work ;-) Thanks to all who responded Jonathan __________________________________________________________________________ SUMMARY OF RESPONSES: The GNU debugger: gdb and xxgdb debugs C, Fortran or whatever Available from: - Any GNU software site - ftp://archie.au/gnu/ - Most major ftp sites - The GNU archive (possibly at MIT) - prep.ai.mit.edu or its mirror sites - gatekeeper.dec.com Fortran check: ftnchek Information from finger ftnchek@mary.fordham.edu Available from: - the netlib site - by ftp from netlib.att.com, directory /netlib/fortran, file ftnchek.tar.gz. It comes complete with a manual and test cases. Installation is straightforward - http://www.fortran.com/fortran/market.html UNIX platforms standard debugger dbx, xdbx, dbm, dde codes need to be compiled with the -g option works in every language Available from: - is free with all UNIX platforms ups Available from: - nearest sunsite (mirror) Linux/devel/debuggers - standard X11/contrib/devel_tools directories g77 Available from: - gatekeeper.dec.com For the PC: Turbo Debugger CodeView _______________________________________________________________ Jonathan Arthur Theoretical Chemistry e-mail: arthur_j@chem.usyd.edu.au School of Chemistry (F11) telephone: +61-2-351-4416 The University of Sydney fax: +61-2-351-3329 NSW 2006 AUSTRALIA URL: http://www.usyd.edu.au/~jarthur/jono.html _______________________________________________________________