From chemistry-request@server.ccl.net Tue Jun 8 06:59:53 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA04136 for ; Tue, 8 Jun 1999 06:59:50 -0400 Message-Id: <199906081059.GAA04136@server.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Tue, 08 Jun 1999 09:50:56 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@ccl.net Date: Tue, 8 Jun 1999 11:53:01 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: Tinker and benzene deriv. Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Xavier Fradera wrote > Hi, > > a few days ago, I asked for a program that could convert sybyl atom types to MM2 or other force- > fields for use in tinker. A. Stevens and C. Gonzalez suggested using the Babel program. > > I have tried babel-1.6. It can read sybyl mol2 fields and write MM2, MM3 and tinker input files, > among other. However, I am not absolutely sure that the atom type conversion is done adequately. > For instance, I have tried translating a mol2 file for a small molecule (benz.mol2) to a tinker > file (benz.xyz) (files are at the end) The atom types generated for a tinker output coincide with > those generated for MM2 and MM3, so i tried running tinker single-point energy calculations using > the MM2, MM3 and tinker parameter sets. In all cases, tinker fails to calculate the energy because > it finds bonds (and torsions) for which it has no parameters, e.g., for the MM2 force-field: > > Undefined Bond Stretching Parameters : > > Type Atom Names Atom Classes > > Bond 1-C 7-C+ 2 30 > Bond 7-C+ 8-N 30 9 > Bond 7-C+ 9-N 30 9 Dear Xavier, I am not a great expert in Tinker, but I as far as I know, Tinker is parametrized specially for proteins. Therefore it is understandable that it lacks parameters in the case of other type of compounds, when it tries to assignate the force field atom types. The xmol type xyz file, which was at the end of your letter, does not contain any info about force field atom types, it contains only elemental symbols and the coordinates and connections. You should try other force field representations, or obtain the missing parameters from the literature. Unfortunately, this happens quite often with "exotic" molecules. best regards tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************