From owner-chemistry@ccl.net Mon Sep 22 03:58:00 2008 From: "Markus Kaukonen markus.kaukonen*o*iki.fi" To: CCL Subject: CCL: Heme parameters Message-Id: <-37780-080922021342-25189-96WeYYwiG8S+wmNZyZnczw:-:server.ccl.net> X-Original-From: "Markus Kaukonen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 22 Sep 2008 09:13:26 +0300 MIME-Version: 1.0 Sent to CCL by: "Markus Kaukonen" [markus.kaukonen]=[iki.fi] Hei, There are old heme parameters for in amber and you can perhaps convert to gromacs. Unfortunately Amber costs money (I guess the same goes for Charmm). The converter may be found in: (but the link did not work for me) http://wiki.gromacs.org/index.php/AMBER and they say you need Amber. You can also check Autenrieth et al. Vol. 25, No. 13 Journal of Computational Chemistry (2004) for Charmm and Amber. Heme there is the one in cytochrome c. This seems to be an issue in gromacs, see http://www.gromacs.org/pipermail/gmx-users/2004-September/012334.html http://www.gromacs.org/pipermail/gmx-users/2006-June/022092.html Terveisin , Markus On Fri, Sep 19, 2008 at 6:38 PM, Mahesh Sundararajan maheshsrajan-x-gmail.com wrote: > Dear CCL members, > > I am unable to find MM heme parameters using > OPLS-aa force field. Please note that I am using GROMACS sofware. > > Can someone help me in this regard. > > Thanks in advance, > > Kind Regards, > Mahesh S > > -- > Dr Mahesh. Sundararajan, > Institute of Physical and Theoretical Chemstry, > University of Bonn, > Bonn - 53115 > Germany > -- --www=http://www.iki.fi/markus.kaukonen --Markus.Kaukonen,iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- From owner-chemistry@ccl.net Mon Sep 22 10:35:00 2008 From: "Christophe Jardin Christophe.Jardin=biochem.uni-erlangen.de" To: CCL Subject: CCL: algorithm sets CAVITY SEARCH Message-Id: <-37781-080922051804-1042-V3d4n1TmY2r55b/z+h+w1g[*]server.ccl.net> X-Original-From: Christophe Jardin Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 22 Sep 2008 10:46:42 +0200 Mime-Version: 1.0 Sent to CCL by: Christophe Jardin [Christophe.Jardin-.-biochem.uni-erlangen.de] Dear CCLers, I'm interested in getting the algorithm sets "CAVITY SEARCH" from Chris Ho and Garland Marshall (Journal of Computer-Aided Molecular Design 1990, 4, 337-354), however I could not found anything on the web to download them nor could come into contact with the authors. Does anyone of you have any idea how to obtain it? Kind regards, christophe -- Dr. Christophe Jardin Institute for Biochemistry University of Erlangen-Nuremberg Germany From owner-chemistry@ccl.net Mon Sep 22 11:10:00 2008 From: "christophe jaridn Christophe.Jardin#,#biochem.uni-erlangen.de" To: CCL Subject: CCL: algorithm sets "CAVITY SEARCH" Message-Id: <-37782-080922061107-4825-bqt6tQbimxDN+2QR9EZrdg(a)server.ccl.net> X-Original-From: "christophe jaridn" Date: Mon, 22 Sep 2008 06:11:03 -0400 Sent to CCL by: "christophe jaridn" [Christophe.Jardin%biochem.uni-erlangen.de] Dear CCLers, I'm interested in getting the algorithm sets "CAVITY SEARCH" from Chris Ho and Garland Marshall (Journal of Computer-Aided Molecular Design 1990, 4, 337-354), however I could not found anything on the web to download them nor could come into contact with the authors. Does anyone of you have any idea how to obtain it? Kind regards, christophe -- Christophe Jardin Institute for Biochemistry University of Erlangen-Nuremberg Germany Christophe.Jardin,biochem.uni-erlangen.de From owner-chemistry@ccl.net Mon Sep 22 19:16:00 2008 From: "David A. Case case#,#biomaps.rutgers.edu" To: CCL Subject: CCL: Heme parameters Message-Id: <-37783-080922084144-31207-jrCl9C53LzcYN7C5MMvWgg#server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 22 Sep 2008 07:34:45 -0400 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case~!~biomaps.rutgers.edu] On Mon, Sep 22, 2008, Markus Kaukonen markus.kaukonen*o*iki.fi wrote: > > > There are old heme parameters for in amber and you can perhaps convert > to gromacs. > Unfortunately Amber costs money (I guess the same goes for Charmm). Just a note: the AmberTools package, which contains all our preparation and analysis tools, as well as codes for nonperiodic simulations, is available without cost (under the GPL license). See http://ambermd.org/#AmberTools. In particular, AmberTools contains the older heme parameters and codes to incorporate them into proteins. Unfortunately, we do not have more up-to-date heme parameters. ...dave case