From chemistry-request-: at :-server.ccl.net Thu Apr 18 09:24:06 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IDO5j09685 for ; Thu, 18 Apr 2002 09:24:05 -0400 Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KGPJLZFUF6000YX3-!at!-unisi.it> for chemistry#* at *#ccl.net; Thu, 18 Apr 2002 12:39:23 +0100 (MET) Date: Thu, 18 Apr 2002 12:39:58 +0200 From: "Nicolas Ferre'" Subject: Re: CCL:Tinker: atom type format for OPLSAA or AMBER Sender: ferre*- at -*unisi.it To: Per Tetzschner Olsen Cc: chemistry {*at*} ccl.net Message-id: <3CBEA27E.6F5C4983 -A_T- unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en References: Hi, In principle, Molden should be used for your purpose (i.e. Tinker's Amber, MM3 and Charmm forcefields), but unfortunatly the actual conversion (pdb -> FF) does not match the last version of Tinker parameters (version 3.9). Let's hope it will be corrected soon (this is a request to G. Schaftenaar, Molden's author), or you can correct the Molden source yourself ... Nicolas Per Tetzschner Olsen wrote: > > Hi CCL > > I am working with the TINKER package (ver. 3.9), because I am > interested in the analytical Gradient and the 'not diagonalized' > Hessian for different kinds of molecular systems. TINKER has > the advantage that you can use several FF. > > Because of no Graphical interface, where you can draw your > molecules I am using Macromodel ver. 7.0 (which is not capable > of calculate the 'not diagonalized' Hessian). > > My problem is when converting from Macromodel format (.dat or PDB) > to TINKER (.xyz) with Babel or pdbxyz.x I received atomtypes > for the molecule saying 0 (with PDBXYZ.x) or the atomtype belonging > to MM3. What about a program which is capable of converting into > OPLSAA, AMBER etc. ???? > > I think of a program of my own, which is capable of reading: > > 1. The atom type (C,H,N.....) > 2. The connectivity > 3. If the atom belongs to a substructure (i.e. DNA-part) > > and convert the atom type into the approriate atom number for > a chosen FF in TINKER. > > I would appreciate if anyone have written or know to the existence > of such program, because manually converting of 500 atoms molecules > takes for ever (or just really long time) > > regards > > Per Tetzschner > > University of Southern Denmark > tetz#* at *#thor.chem.sdu.dk > +45-65502570 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY#* at *#ccl.net -- To Everybody | CHEMISTRY-REQUEST#* at *#ccl.net -- To Admins > MAILSERV -A_T- ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH #at# ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl # - at - # ccl.net -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre ^%at%^ unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~